Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 15:14:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8faz_28961/10_2023/8faz_28961_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8faz_28961/10_2023/8faz_28961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8faz_28961/10_2023/8faz_28961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8faz_28961/10_2023/8faz_28961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8faz_28961/10_2023/8faz_28961_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8faz_28961/10_2023/8faz_28961_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 50 5.16 5 C 4619 2.51 5 N 1275 2.21 5 O 1377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 7331 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 570 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "C" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2470 Classifications: {'peptide': 314} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 301} Chain breaks: 2 Chain: "D" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2288 Classifications: {'peptide': 303} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 294} Chain breaks: 2 Chain: "X" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1912 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 229} Chain breaks: 3 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.46, per 1000 atoms: 0.61 Number of scatterers: 7331 At special positions: 0 Unit cell: (68.73, 80.91, 111.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 8 15.00 Mg 2 11.99 O 1377 8.00 N 1275 7.00 C 4619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.0 seconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 5 sheets defined 44.5% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'B' and resid 13 through 22 removed outlier: 4.121A pdb=" N HIS B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 35 through 41 removed outlier: 4.061A pdb=" N LYS B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 59 removed outlier: 3.532A pdb=" N ALA B 59 " --> pdb=" O MET B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 74 Processing helix chain 'C' and resid 14 through 16 No H-bonds generated for 'chain 'C' and resid 14 through 16' Processing helix chain 'C' and resid 21 through 29 Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 54 through 66 Processing helix chain 'C' and resid 87 through 96 Processing helix chain 'C' and resid 105 through 111 Processing helix chain 'C' and resid 131 through 143 removed outlier: 3.536A pdb=" N VAL C 140 " --> pdb=" O MET C 136 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 166 through 186 removed outlier: 3.883A pdb=" N GLU C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 197 removed outlier: 4.103A pdb=" N ALA C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 197 " --> pdb=" O ARG C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 255 through 276 Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'D' and resid 14 through 23 removed outlier: 3.650A pdb=" N HIS D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 33 Processing helix chain 'D' and resid 36 through 43 Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 68 through 76 Processing helix chain 'D' and resid 87 through 90 No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 113 through 126 Processing helix chain 'D' and resid 143 through 153 Processing helix chain 'D' and resid 157 through 166 removed outlier: 3.553A pdb=" N ALA D 161 " --> pdb=" O GLU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 191 Processing helix chain 'D' and resid 208 through 215 Proline residue: D 214 - end of helix Processing helix chain 'D' and resid 222 through 239 Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'X' and resid 24 through 27 No H-bonds generated for 'chain 'X' and resid 24 through 27' Processing helix chain 'X' and resid 54 through 66 Processing helix chain 'X' and resid 89 through 99 Processing helix chain 'X' and resid 105 through 114 removed outlier: 3.683A pdb=" N ARG X 114 " --> pdb=" O TYR X 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 139 removed outlier: 3.694A pdb=" N GLU X 134 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER X 135 " --> pdb=" O TYR X 131 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N MET X 136 " --> pdb=" O SER X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 155 through 161 Processing helix chain 'X' and resid 166 through 169 No H-bonds generated for 'chain 'X' and resid 166 through 169' Processing helix chain 'X' and resid 171 through 187 Processing helix chain 'X' and resid 229 through 234 removed outlier: 3.959A pdb=" N LEU X 234 " --> pdb=" O ALA X 230 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 336 through 338 removed outlier: 6.702A pdb=" N ARG C 312 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU C 154 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL C 239 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 156 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL C 241 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 158 " --> pdb=" O VAL C 241 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 340 through 342 Processing sheet with id= C, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.362A pdb=" N ARG D 275 " --> pdb=" O ALA D 296 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 274 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL D 245 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE D 105 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL D 247 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLY D 107 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN D 249 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASN D 131 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL D 203 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU D 133 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL D 205 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL D 135 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 251 through 253 Processing sheet with id= E, first strand: chain 'X' and resid 276 through 280 removed outlier: 4.168A pdb=" N PHE X 269 " --> pdb=" O CYS X 280 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER X 264 " --> pdb=" O CYS X 259 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS X 237 " --> pdb=" O ILE X 43 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY X 48 " --> pdb=" O THR X 195 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU X 148 " --> pdb=" O PHE X 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR X 194 " --> pdb=" O LEU X 148 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLU X 77 " --> pdb=" O CYS X 144 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU X 146 " --> pdb=" O GLU X 77 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU X 79 " --> pdb=" O LEU X 146 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU X 148 " --> pdb=" O LEU X 79 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE X 81 " --> pdb=" O LEU X 148 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2410 1.34 - 1.46: 1539 1.46 - 1.58: 3409 1.58 - 1.69: 13 1.69 - 1.81: 72 Bond restraints: 7443 Sorted by residual: bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" O3A ANP X 301 " pdb=" PB ANP X 301 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" N3B ANP X 301 " pdb=" PG ANP X 301 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O5' ANP D 401 " pdb=" PA ANP D 401 " ideal model delta sigma weight residual 1.655 1.579 0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 7438 not shown) Histogram of bond angle deviations from ideal: 100.05 - 107.22: 217 107.22 - 114.39: 4545 114.39 - 121.57: 3603 121.57 - 128.74: 1645 128.74 - 135.91: 47 Bond angle restraints: 10057 Sorted by residual: angle pdb=" PB ANP X 301 " pdb=" N3B ANP X 301 " pdb=" PG ANP X 301 " ideal model delta sigma weight residual 126.95 109.59 17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 109.85 17.10 3.00e+00 1.11e-01 3.25e+01 angle pdb=" N ILE C 183 " pdb=" CA ILE C 183 " pdb=" C ILE C 183 " ideal model delta sigma weight residual 112.80 108.50 4.30 1.15e+00 7.56e-01 1.40e+01 angle pdb=" O1B ANP D 401 " pdb=" PB ANP D 401 " pdb=" O2B ANP D 401 " ideal model delta sigma weight residual 120.08 109.22 10.86 3.00e+00 1.11e-01 1.31e+01 angle pdb=" O1B ANP X 301 " pdb=" PB ANP X 301 " pdb=" O2B ANP X 301 " ideal model delta sigma weight residual 120.08 109.40 10.68 3.00e+00 1.11e-01 1.27e+01 ... (remaining 10052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.63: 4384 26.63 - 53.26: 91 53.26 - 79.90: 8 79.90 - 106.53: 2 106.53 - 133.16: 1 Dihedral angle restraints: 4486 sinusoidal: 1823 harmonic: 2663 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 73.16 -133.16 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -147.03 87.03 1 2.00e+01 2.50e-03 2.28e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -0.52 -59.48 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 4483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1038 0.056 - 0.112: 129 0.112 - 0.167: 8 0.167 - 0.223: 0 0.223 - 0.279: 2 Chirality restraints: 1177 Sorted by residual: chirality pdb=" C3' ANP X 301 " pdb=" C2' ANP X 301 " pdb=" C4' ANP X 301 " pdb=" O3' ANP X 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ILE C 144 " pdb=" N ILE C 144 " pdb=" C ILE C 144 " pdb=" CB ILE C 144 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1174 not shown) Planarity restraints: 1258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY X 48 " -0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO X 49 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO X 49 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO X 49 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 342 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO C 343 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 343 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 343 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 42 " 0.017 5.00e-02 4.00e+02 2.50e-02 9.98e-01 pdb=" N PRO C 43 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " 0.014 5.00e-02 4.00e+02 ... (remaining 1255 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 85 2.57 - 3.15: 6025 3.15 - 3.73: 12124 3.73 - 4.32: 17227 4.32 - 4.90: 27975 Nonbonded interactions: 63436 Sorted by model distance: nonbonded pdb=" OG1 THR X 55 " pdb="MG MG X 302 " model vdw 1.986 2.170 nonbonded pdb=" O3G ANP D 401 " pdb="MG MG D 402 " model vdw 1.992 2.170 nonbonded pdb=" O1G ANP X 301 " pdb="MG MG X 302 " model vdw 2.013 2.170 nonbonded pdb=" OG1 THR D 114 " pdb="MG MG D 402 " model vdw 2.013 2.170 nonbonded pdb=" O1B ANP X 301 " pdb="MG MG X 302 " model vdw 2.027 2.170 ... (remaining 63431 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.900 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.300 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 7443 Z= 0.284 Angle : 0.616 17.364 10057 Z= 0.269 Chirality : 0.039 0.279 1177 Planarity : 0.003 0.028 1258 Dihedral : 10.771 133.159 2758 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.50 % Allowed : 2.74 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.28), residues: 904 helix: 0.68 (0.25), residues: 417 sheet: 0.30 (0.45), residues: 151 loop : -0.19 (0.34), residues: 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 0.846 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 193 average time/residue: 1.1715 time to fit residues: 239.0702 Evaluate side-chains 148 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.1166 time to fit residues: 1.2650 ------------------------------------------------------------------------------- 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: 0.9980 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN C 263 ASN C 267 GLN D 60 GLN D 301 GLN X 252 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7443 Z= 0.218 Angle : 0.564 6.579 10057 Z= 0.273 Chirality : 0.041 0.143 1177 Planarity : 0.004 0.041 1258 Dihedral : 6.471 96.230 1008 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.36 % Allowed : 12.44 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.28), residues: 904 helix: 0.88 (0.25), residues: 434 sheet: -0.28 (0.45), residues: 139 loop : -0.14 (0.35), residues: 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 0.772 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 168 average time/residue: 1.1500 time to fit residues: 204.3246 Evaluate side-chains 159 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.6192 time to fit residues: 3.2129 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 11 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN X 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7443 Z= 0.305 Angle : 0.587 7.215 10057 Z= 0.286 Chirality : 0.043 0.234 1177 Planarity : 0.004 0.050 1258 Dihedral : 5.698 64.489 1008 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.48 % Allowed : 14.05 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.28), residues: 904 helix: 0.89 (0.25), residues: 427 sheet: -0.27 (0.43), residues: 150 loop : -0.13 (0.35), residues: 327 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 0.889 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 164 average time/residue: 1.1752 time to fit residues: 203.7648 Evaluate side-chains 159 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 6 average time/residue: 0.6255 time to fit residues: 5.3328 ------------------------------------------------------------------------------- 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: 0.9990 chunk 42 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 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 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN X 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7443 Z= 0.214 Angle : 0.558 6.979 10057 Z= 0.268 Chirality : 0.042 0.184 1177 Planarity : 0.004 0.052 1258 Dihedral : 5.127 51.784 1008 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.49 % Allowed : 15.55 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.28), residues: 904 helix: 1.01 (0.25), residues: 430 sheet: -0.26 (0.43), residues: 150 loop : -0.09 (0.35), residues: 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 0.884 Fit side-chains outliers start: 20 outliers final: 8 residues processed: 169 average time/residue: 1.0821 time to fit residues: 194.1286 Evaluate side-chains 157 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 0.764 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 3 average time/residue: 0.1211 time to fit residues: 1.6080 ------------------------------------------------------------------------------- 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: 0.7980 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN X 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7443 Z= 0.232 Angle : 0.581 7.270 10057 Z= 0.279 Chirality : 0.041 0.195 1177 Planarity : 0.004 0.062 1258 Dihedral : 5.030 52.895 1008 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.61 % Allowed : 17.29 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.28), residues: 904 helix: 1.04 (0.25), residues: 436 sheet: -0.40 (0.42), residues: 156 loop : -0.24 (0.36), residues: 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 0.901 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 166 average time/residue: 1.1136 time to fit residues: 196.0263 Evaluate side-chains 155 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 6 average time/residue: 0.1135 time to fit residues: 2.2039 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 7 optimal weight: 0.0030 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.0010 chunk 84 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7443 Z= 0.167 Angle : 0.574 8.080 10057 Z= 0.275 Chirality : 0.042 0.239 1177 Planarity : 0.004 0.045 1258 Dihedral : 4.904 54.481 1008 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.87 % Allowed : 18.53 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.29), residues: 904 helix: 1.16 (0.25), residues: 436 sheet: -0.30 (0.43), residues: 154 loop : -0.21 (0.36), residues: 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 0.908 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 166 average time/residue: 1.1491 time to fit residues: 202.0852 Evaluate side-chains 143 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 4 average time/residue: 0.4626 time to fit residues: 3.2801 ------------------------------------------------------------------------------- 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: 0.7980 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 HIS D 301 GLN X 252 GLN X 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7443 Z= 0.230 Angle : 0.614 9.241 10057 Z= 0.291 Chirality : 0.043 0.274 1177 Planarity : 0.004 0.043 1258 Dihedral : 4.974 55.080 1008 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.99 % Allowed : 18.41 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.28), residues: 904 helix: 1.15 (0.25), residues: 434 sheet: -0.35 (0.42), residues: 157 loop : -0.19 (0.35), residues: 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 0.907 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 151 average time/residue: 1.1728 time to fit residues: 187.3733 Evaluate side-chains 146 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 6 average time/residue: 0.3357 time to fit residues: 3.5216 ------------------------------------------------------------------------------- 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: 0.8980 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 76 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7443 Z= 0.196 Angle : 0.608 10.910 10057 Z= 0.291 Chirality : 0.042 0.207 1177 Planarity : 0.003 0.049 1258 Dihedral : 4.964 55.769 1008 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.49 % Allowed : 20.02 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.28), residues: 904 helix: 1.22 (0.25), residues: 432 sheet: -0.28 (0.42), residues: 155 loop : -0.20 (0.35), residues: 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 0.913 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 151 average time/residue: 1.2220 time to fit residues: 194.7592 Evaluate side-chains 140 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.872 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 3 average time/residue: 0.0828 time to fit residues: 1.6215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.6769 > 50: distance: 99 - 213: 13.821 distance: 109 - 216: 20.850 distance: 112 - 232: 18.257 distance: 162 - 179: 5.592 distance: 168 - 187: 11.641 distance: 175 - 179: 4.188 distance: 180 - 181: 3.427 distance: 180 - 183: 6.889 distance: 181 - 182: 12.327 distance: 181 - 187: 6.493 distance: 183 - 184: 5.207 distance: 184 - 185: 8.047 distance: 184 - 186: 13.725 distance: 187 - 188: 7.037 distance: 188 - 189: 11.713 distance: 189 - 190: 5.111 distance: 189 - 191: 12.296 distance: 191 - 192: 11.664 distance: 192 - 193: 13.423 distance: 192 - 195: 8.328 distance: 193 - 194: 3.291 distance: 193 - 202: 6.931 distance: 195 - 196: 6.984 distance: 196 - 197: 10.325 distance: 197 - 198: 7.378 distance: 198 - 199: 17.298 distance: 199 - 200: 18.227 distance: 199 - 201: 18.727 distance: 202 - 203: 6.461 distance: 203 - 206: 3.768 distance: 204 - 213: 19.585 distance: 206 - 207: 10.142 distance: 207 - 208: 21.100 distance: 207 - 209: 12.785 distance: 208 - 210: 16.231 distance: 209 - 211: 10.333 distance: 210 - 212: 14.619 distance: 211 - 212: 14.052 distance: 213 - 214: 4.607 distance: 214 - 215: 5.521 distance: 215 - 216: 7.297 distance: 215 - 224: 6.118 distance: 217 - 218: 8.612 distance: 218 - 219: 8.864 distance: 219 - 221: 6.816 distance: 220 - 222: 6.704 distance: 221 - 223: 5.171 distance: 222 - 223: 7.031 distance: 224 - 225: 13.760 distance: 225 - 226: 5.756 distance: 225 - 228: 6.075 distance: 226 - 227: 5.136 distance: 226 - 232: 12.053 distance: 228 - 229: 5.508 distance: 229 - 231: 12.951 distance: 232 - 233: 20.122 distance: 233 - 234: 14.149 distance: 233 - 236: 17.155 distance: 234 - 235: 11.442 distance: 234 - 239: 7.373 distance: 236 - 237: 9.206 distance: 236 - 238: 39.079 distance: 239 - 240: 13.052 distance: 240 - 241: 16.945 distance: 240 - 243: 6.059 distance: 241 - 242: 15.008 distance: 241 - 251: 17.759 distance: 243 - 244: 11.556 distance: 244 - 245: 8.997 distance: 244 - 246: 9.868 distance: 245 - 247: 9.576 distance: 246 - 248: 5.974 distance: 247 - 249: 10.922 distance: 248 - 249: 4.367 distance: 249 - 250: 6.760 distance: 251 - 252: 4.995 distance: 252 - 253: 3.214 distance: 252 - 255: 10.277 distance: 253 - 257: 8.116 distance: 255 - 256: 15.248 distance: 257 - 258: 9.469 distance: 258 - 259: 8.640 distance: 258 - 261: 6.597 distance: 259 - 260: 5.108 distance: 259 - 263: 18.391 distance: 261 - 262: 3.705