Starting phenix.real_space_refine on Wed Mar 12 06:04:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wog_37686/03_2025/8wog_37686_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wog_37686/03_2025/8wog_37686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wog_37686/03_2025/8wog_37686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wog_37686/03_2025/8wog_37686.map" model { file = "/net/cci-nas-00/data/ceres_data/8wog_37686/03_2025/8wog_37686_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wog_37686/03_2025/8wog_37686_trim.cif" } resolution = 2.97 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= -0.001 sd= 0.110 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: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 4721 2.51 5 N 1242 2.21 5 O 1367 1.98 5 H 2 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7384 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2538 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 12, 'TRANS': 298} Chain: "C" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1834 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2568 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {'SIN': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 4.53, per 1000 atoms: 0.61 Number of scatterers: 7384 At special positions: 0 Unit cell: (70.55, 102, 138.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1367 8.00 N 1242 7.00 C 4721 6.00 H 2 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 11 " - pdb=" SG CYS A 268 " distance=2.04 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 172 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.63 Conformation dependent library (CDL) restraints added in 916.4 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1764 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 45.4% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 10 through 24 removed outlier: 3.574A pdb=" N ALA A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 46 Processing helix chain 'A' and resid 56 through 74 Processing helix chain 'A' and resid 75 through 86 removed outlier: 4.214A pdb=" N LEU A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 126 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.933A pdb=" N LYS A 135 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 155 removed outlier: 3.591A pdb=" N LEU A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 196 through 217 Processing helix chain 'A' and resid 228 through 259 removed outlier: 3.617A pdb=" N VAL A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Proline residue: A 247 - end of helix removed outlier: 3.744A pdb=" N ASN A 253 " --> pdb=" O HIS A 249 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 286 Proline residue: A 282 - end of helix removed outlier: 3.846A pdb=" N PHE A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 299 through 312 Processing helix chain 'C' and resid 7 through 31 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.751A pdb=" N ILE C 49 " --> pdb=" O GLY C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.571A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.678A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'D' and resid 4 through 8 Processing helix chain 'D' and resid 10 through 25 removed outlier: 3.563A pdb=" N CYS D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'E' and resid 9 through 22 Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 45 through 48 removed outlier: 3.636A pdb=" N ASP E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 45 through 48' Processing helix chain 'E' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 166 removed outlier: 3.623A pdb=" N THR A 166 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 184 through 190 removed outlier: 6.248A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL C 201 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU C 38 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.792A pdb=" N ARG D 49 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS D 317 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 62 removed outlier: 3.599A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105 removed outlier: 7.058A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 153 removed outlier: 6.769A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE D 151 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLN D 156 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS D 166 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.969A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR D 221 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU D 210 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.520A pdb=" N CYS D 250 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR D 263 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU D 252 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN D 259 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.795A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1071 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: 1.83 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 2 1.04 - 1.23: 60 1.23 - 1.43: 3119 1.43 - 1.62: 4278 1.62 - 1.82: 74 Bond restraints: 7533 Sorted by residual: bond pdb=" CA ILE A 278 " pdb=" C ILE A 278 " ideal model delta sigma weight residual 1.522 1.435 0.086 1.38e-02 5.25e+03 3.92e+01 bond pdb=" CA SER A 275 " pdb=" CB SER A 275 " ideal model delta sigma weight residual 1.528 1.458 0.070 1.56e-02 4.11e+03 2.03e+01 bond pdb=" CA VAL A 279 " pdb=" C VAL A 279 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.46e-02 4.69e+03 1.99e+01 bond pdb=" CA TYR A 277 " pdb=" CB TYR A 277 " ideal model delta sigma weight residual 1.529 1.460 0.069 1.55e-02 4.16e+03 1.99e+01 bond pdb=" C TYR A 277 " pdb=" O TYR A 277 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.15e-02 7.56e+03 1.92e+01 ... (remaining 7528 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 10068 1.88 - 3.75: 117 3.75 - 5.63: 9 5.63 - 7.50: 6 7.50 - 9.38: 1 Bond angle restraints: 10201 Sorted by residual: angle pdb=" C VAL A 279 " pdb=" CA VAL A 279 " pdb=" CB VAL A 279 " ideal model delta sigma weight residual 112.26 102.88 9.38 1.62e+00 3.81e-01 3.35e+01 angle pdb=" C SER A 275 " pdb=" N PHE A 276 " pdb=" CA PHE A 276 " ideal model delta sigma weight residual 120.29 113.88 6.41 1.42e+00 4.96e-01 2.04e+01 angle pdb=" C VAL A 272 " pdb=" CA VAL A 272 " pdb=" CB VAL A 272 " ideal model delta sigma weight residual 111.97 106.22 5.75 1.28e+00 6.10e-01 2.02e+01 angle pdb=" C ILE A 278 " pdb=" CA ILE A 278 " pdb=" CB ILE A 278 " ideal model delta sigma weight residual 112.16 105.88 6.28 1.55e+00 4.16e-01 1.64e+01 angle pdb=" CA TYR A 277 " pdb=" C TYR A 277 " pdb=" N ILE A 278 " ideal model delta sigma weight residual 117.07 121.45 -4.38 1.14e+00 7.69e-01 1.48e+01 ... (remaining 10196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3886 17.98 - 35.95: 458 35.95 - 53.93: 113 53.93 - 71.90: 30 71.90 - 89.88: 3 Dihedral angle restraints: 4490 sinusoidal: 1768 harmonic: 2722 Sorted by residual: dihedral pdb=" CA ASP D 38 " pdb=" CB ASP D 38 " pdb=" CG ASP D 38 " pdb=" OD1 ASP D 38 " ideal model delta sinusoidal sigma weight residual -30.00 -89.12 59.12 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CB GLU D 172 " pdb=" CG GLU D 172 " pdb=" CD GLU D 172 " pdb=" OE1 GLU D 172 " ideal model delta sinusoidal sigma weight residual 0.00 89.88 -89.88 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP A 167 " pdb=" CB ASP A 167 " pdb=" CG ASP A 167 " pdb=" OD1 ASP A 167 " ideal model delta sinusoidal sigma weight residual -30.00 -85.44 55.44 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 4487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 935 0.047 - 0.095: 175 0.095 - 0.142: 53 0.142 - 0.190: 2 0.190 - 0.237: 1 Chirality restraints: 1166 Sorted by residual: chirality pdb=" CA PHE A 276 " pdb=" N PHE A 276 " pdb=" C PHE A 276 " pdb=" CB PHE A 276 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA VAL A 279 " pdb=" N VAL A 279 " pdb=" C VAL A 279 " pdb=" CB VAL A 279 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA VAL A 272 " pdb=" N VAL A 272 " pdb=" C VAL A 272 " pdb=" CB VAL A 272 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1163 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 198 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 199 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 273 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.64e+00 pdb=" C ILE A 273 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE A 273 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A 274 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 21 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C ARG C 21 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG C 21 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN C 22 " -0.008 2.00e-02 2.50e+03 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.40: 22 2.40 - 2.95: 3449 2.95 - 3.50: 8345 3.50 - 4.05: 12786 4.05 - 4.60: 19851 Nonbonded interactions: 44453 Sorted by model distance: nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 1.844 2.800 nonbonded pdb=" OG SER D 245 " pdb=" OD1 ASP D 247 " model vdw 1.963 2.800 nonbonded pdb=" O ARG D 68 " pdb=" OG SER D 84 " model vdw 2.040 2.800 nonbonded pdb=" OG SER D 74 " pdb=" OD2 ASP D 76 " model vdw 2.115 2.800 nonbonded pdb=" NH2 ARG A 217 " pdb=" OD1 ASP C 341 " model vdw 2.141 2.950 ... (remaining 44448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.880 Find NCS groups from input model: 0.080 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:10.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 0.086 7531 Z= 0.236 Angle : 0.498 9.379 10200 Z= 0.308 Chirality : 0.041 0.237 1166 Planarity : 0.003 0.043 1288 Dihedral : 16.624 89.877 2720 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.96 % Allowed : 23.55 % Favored : 73.49 % 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: 0.49 (0.29), residues: 916 helix: 1.72 (0.27), residues: 390 sheet: 0.16 (0.39), residues: 173 loop : -1.17 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 82 HIS 0.007 0.001 HIS D 183 PHE 0.009 0.001 PHE C 189 TYR 0.015 0.001 TYR A 277 ARG 0.008 0.000 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6618 (mmp-170) REVERT: A 209 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7806 (mttm) outliers start: 24 outliers final: 17 residues processed: 122 average time/residue: 1.1600 time to fit residues: 149.7198 Evaluate side-chains 116 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 333 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.0570 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 313 ASN C 241 ASN C 255 ASN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN D 340 ASN E 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.156249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107166 restraints weight = 8110.801| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.52 r_work: 0.3059 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7531 Z= 0.185 Angle : 0.430 5.037 10200 Z= 0.238 Chirality : 0.040 0.132 1166 Planarity : 0.003 0.039 1288 Dihedral : 5.941 58.707 1040 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.67 % Allowed : 19.61 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.29), residues: 916 helix: 2.46 (0.27), residues: 396 sheet: 0.26 (0.40), residues: 169 loop : -1.29 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 82 HIS 0.004 0.001 HIS D 183 PHE 0.010 0.001 PHE C 189 TYR 0.014 0.001 TYR A 107 ARG 0.004 0.000 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 102 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6629 (mmp-170) REVERT: A 90 TYR cc_start: 0.6311 (m-80) cc_final: 0.6101 (m-80) REVERT: A 189 MET cc_start: 0.8025 (tpt) cc_final: 0.7805 (mmm) REVERT: A 263 TRP cc_start: 0.6616 (OUTLIER) cc_final: 0.6316 (t-100) REVERT: D 188 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8219 (mmm) REVERT: D 258 ASP cc_start: 0.8386 (t0) cc_final: 0.8128 (t0) outliers start: 46 outliers final: 22 residues processed: 128 average time/residue: 1.1355 time to fit residues: 153.6934 Evaluate side-chains 120 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 292 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.155763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.104175 restraints weight = 8213.956| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.71 r_work: 0.3015 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7531 Z= 0.287 Angle : 0.484 6.302 10200 Z= 0.264 Chirality : 0.042 0.138 1166 Planarity : 0.003 0.039 1288 Dihedral : 5.638 58.905 1025 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 6.66 % Allowed : 19.11 % Favored : 74.23 % 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: 0.92 (0.28), residues: 916 helix: 2.55 (0.27), residues: 395 sheet: -0.05 (0.40), residues: 167 loop : -1.37 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 82 HIS 0.006 0.001 HIS D 183 PHE 0.015 0.002 PHE A 115 TYR 0.017 0.001 TYR A 107 ARG 0.005 0.000 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 97 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7757 (t80) REVERT: A 81 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6528 (mmp-170) REVERT: A 90 TYR cc_start: 0.6695 (m-80) cc_final: 0.6367 (m-80) REVERT: A 263 TRP cc_start: 0.6375 (OUTLIER) cc_final: 0.6024 (t-100) REVERT: C 242 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6648 (mtt180) REVERT: D 82 TRP cc_start: 0.9269 (OUTLIER) cc_final: 0.9000 (m100) REVERT: D 188 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8440 (mmm) REVERT: D 189 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8887 (p) REVERT: D 198 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8799 (mp) REVERT: D 214 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7104 (mpp-170) REVERT: D 258 ASP cc_start: 0.8331 (t0) cc_final: 0.8045 (t0) outliers start: 54 outliers final: 25 residues processed: 130 average time/residue: 1.1297 time to fit residues: 155.4477 Evaluate side-chains 129 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 82 TRP Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 317 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 chunk 21 optimal weight: 0.4980 chunk 64 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN E 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.159620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109770 restraints weight = 8218.752| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.72 r_work: 0.3081 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7531 Z= 0.125 Angle : 0.380 4.887 10200 Z= 0.212 Chirality : 0.039 0.132 1166 Planarity : 0.002 0.033 1288 Dihedral : 5.163 57.832 1023 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.56 % Allowed : 21.09 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.29), residues: 916 helix: 2.89 (0.27), residues: 396 sheet: 0.17 (0.40), residues: 166 loop : -1.25 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 82 HIS 0.005 0.001 HIS D 183 PHE 0.008 0.001 PHE C 189 TYR 0.010 0.001 TYR A 107 ARG 0.005 0.000 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6589 (mmp-170) REVERT: A 90 TYR cc_start: 0.6481 (m-80) cc_final: 0.6201 (m-80) REVERT: A 265 GLN cc_start: 0.5774 (OUTLIER) cc_final: 0.5410 (mp10) REVERT: C 33 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8277 (mt-10) REVERT: D 188 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8222 (mmm) REVERT: D 189 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8778 (p) REVERT: D 198 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8756 (mp) REVERT: D 258 ASP cc_start: 0.8372 (t0) cc_final: 0.8091 (t0) outliers start: 37 outliers final: 17 residues processed: 123 average time/residue: 1.1931 time to fit residues: 155.1034 Evaluate side-chains 118 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 292 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 33 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 38 optimal weight: 0.0270 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN D 340 ASN E 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.156244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104763 restraints weight = 8161.702| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.70 r_work: 0.3061 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7531 Z= 0.159 Angle : 0.401 4.920 10200 Z= 0.221 Chirality : 0.039 0.132 1166 Planarity : 0.003 0.032 1288 Dihedral : 4.881 57.953 1018 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.93 % Allowed : 21.09 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.29), residues: 916 helix: 2.94 (0.27), residues: 394 sheet: 0.03 (0.39), residues: 172 loop : -1.19 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 82 HIS 0.005 0.001 HIS D 183 PHE 0.009 0.001 PHE C 189 TYR 0.013 0.001 TYR A 107 ARG 0.006 0.000 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6499 (mmp-170) REVERT: A 90 TYR cc_start: 0.6493 (m-80) cc_final: 0.6166 (m-80) REVERT: A 265 GLN cc_start: 0.5802 (OUTLIER) cc_final: 0.5469 (mp10) REVERT: C 33 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8258 (mt-10) REVERT: D 189 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.8797 (p) REVERT: D 214 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.6989 (mpp-170) REVERT: D 258 ASP cc_start: 0.8327 (t0) cc_final: 0.8093 (t0) outliers start: 40 outliers final: 24 residues processed: 121 average time/residue: 1.1172 time to fit residues: 143.5597 Evaluate side-chains 124 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.103794 restraints weight = 8217.487| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.70 r_work: 0.3018 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7531 Z= 0.331 Angle : 0.498 6.678 10200 Z= 0.268 Chirality : 0.042 0.137 1166 Planarity : 0.003 0.034 1288 Dihedral : 5.208 58.511 1018 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 6.04 % Allowed : 20.59 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.29), residues: 916 helix: 2.66 (0.27), residues: 394 sheet: -0.07 (0.39), residues: 167 loop : -1.35 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 82 HIS 0.006 0.001 HIS D 183 PHE 0.015 0.002 PHE A 115 TYR 0.017 0.001 TYR A 107 ARG 0.006 0.000 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 93 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.7657 (t80) REVERT: A 81 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6486 (mmp-170) REVERT: A 217 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.5861 (tmm160) REVERT: C 33 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8514 (mt-10) REVERT: D 82 TRP cc_start: 0.9280 (OUTLIER) cc_final: 0.9022 (m100) REVERT: D 189 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8886 (p) REVERT: D 214 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7138 (mpp-170) outliers start: 49 outliers final: 31 residues processed: 123 average time/residue: 1.1670 time to fit residues: 152.6537 Evaluate side-chains 127 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 82 TRP Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 40 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 90 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.158738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108315 restraints weight = 8171.735| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.93 r_work: 0.3029 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7531 Z= 0.141 Angle : 0.399 4.876 10200 Z= 0.219 Chirality : 0.039 0.134 1166 Planarity : 0.003 0.032 1288 Dihedral : 4.961 58.304 1018 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.69 % Allowed : 22.44 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.29), residues: 916 helix: 2.90 (0.27), residues: 394 sheet: -0.07 (0.39), residues: 167 loop : -1.25 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 82 HIS 0.006 0.001 HIS D 183 PHE 0.009 0.001 PHE D 292 TYR 0.011 0.001 TYR A 107 ARG 0.008 0.000 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6526 (mmp-170) REVERT: A 217 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6039 (tmm160) REVERT: A 265 GLN cc_start: 0.5876 (OUTLIER) cc_final: 0.5462 (mp10) REVERT: C 33 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8340 (mt-10) REVERT: D 189 SER cc_start: 0.9036 (OUTLIER) cc_final: 0.8822 (p) outliers start: 38 outliers final: 27 residues processed: 121 average time/residue: 1.1839 time to fit residues: 151.6075 Evaluate side-chains 125 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 69 optimal weight: 0.0070 chunk 81 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 19 optimal weight: 0.0050 overall best weight: 0.4412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN E 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.160590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110790 restraints weight = 8176.702| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.73 r_work: 0.3091 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 7531 Z= 0.112 Angle : 0.372 4.874 10200 Z= 0.205 Chirality : 0.038 0.130 1166 Planarity : 0.002 0.031 1288 Dihedral : 4.731 58.071 1018 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.95 % Allowed : 23.43 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.29), residues: 916 helix: 3.11 (0.27), residues: 394 sheet: -0.02 (0.38), residues: 177 loop : -1.11 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 82 HIS 0.005 0.001 HIS D 183 PHE 0.008 0.001 PHE C 189 TYR 0.010 0.001 TYR A 107 ARG 0.007 0.000 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.762 Fit side-chains REVERT: A 81 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6585 (mmp-170) REVERT: A 217 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.5988 (tmm160) REVERT: A 265 GLN cc_start: 0.5800 (OUTLIER) cc_final: 0.5453 (mp10) REVERT: C 33 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8235 (mt-10) REVERT: D 38 ASP cc_start: 0.8254 (m-30) cc_final: 0.7933 (t0) REVERT: D 189 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8814 (p) outliers start: 32 outliers final: 23 residues processed: 121 average time/residue: 1.2148 time to fit residues: 155.8588 Evaluate side-chains 121 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 55 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 chunk 89 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN E 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.160315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109936 restraints weight = 8228.266| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.74 r_work: 0.3085 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7531 Z= 0.137 Angle : 0.392 5.515 10200 Z= 0.215 Chirality : 0.038 0.135 1166 Planarity : 0.003 0.035 1288 Dihedral : 4.373 53.971 1015 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.19 % Allowed : 23.30 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.29), residues: 916 helix: 3.12 (0.27), residues: 394 sheet: 0.06 (0.39), residues: 165 loop : -1.16 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 82 HIS 0.005 0.001 HIS D 183 PHE 0.009 0.001 PHE C 189 TYR 0.012 0.001 TYR A 107 ARG 0.009 0.000 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.789 Fit side-chains REVERT: A 81 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6575 (mmp-170) REVERT: A 217 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.5976 (tmm160) REVERT: A 265 GLN cc_start: 0.5831 (OUTLIER) cc_final: 0.5415 (mp10) REVERT: C 20 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7419 (m-30) REVERT: C 33 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8234 (mt-10) REVERT: D 38 ASP cc_start: 0.8233 (m-30) cc_final: 0.7931 (t0) REVERT: D 189 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8814 (p) REVERT: D 214 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6918 (mpp-170) outliers start: 34 outliers final: 24 residues processed: 118 average time/residue: 1.2095 time to fit residues: 150.9412 Evaluate side-chains 126 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.156987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105825 restraints weight = 8239.746| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.70 r_work: 0.3064 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7531 Z= 0.141 Angle : 0.395 5.842 10200 Z= 0.216 Chirality : 0.039 0.132 1166 Planarity : 0.003 0.032 1288 Dihedral : 4.379 53.903 1015 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.19 % Allowed : 23.30 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.29), residues: 916 helix: 3.11 (0.27), residues: 394 sheet: 0.05 (0.39), residues: 165 loop : -1.14 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 82 HIS 0.005 0.001 HIS D 183 PHE 0.009 0.001 PHE C 189 TYR 0.013 0.001 TYR A 107 ARG 0.007 0.000 ARG C 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.829 Fit side-chains REVERT: A 81 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6543 (mmp-170) REVERT: A 217 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.5931 (tmm160) REVERT: A 265 GLN cc_start: 0.5805 (OUTLIER) cc_final: 0.5459 (mp10) REVERT: C 33 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: D 38 ASP cc_start: 0.8235 (m-30) cc_final: 0.7921 (t0) REVERT: D 189 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8807 (p) REVERT: D 214 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.6860 (mpp-170) outliers start: 34 outliers final: 24 residues processed: 119 average time/residue: 1.2067 time to fit residues: 151.8190 Evaluate side-chains 124 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 0.0060 chunk 85 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.156892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105869 restraints weight = 8140.916| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.68 r_work: 0.3077 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7531 Z= 0.143 Angle : 0.399 5.498 10200 Z= 0.218 Chirality : 0.039 0.132 1166 Planarity : 0.002 0.031 1288 Dihedral : 4.384 53.777 1015 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.07 % Allowed : 23.55 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.29), residues: 916 helix: 3.14 (0.27), residues: 394 sheet: 0.05 (0.39), residues: 165 loop : -1.14 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 82 HIS 0.005 0.001 HIS D 183 PHE 0.009 0.001 PHE C 189 TYR 0.013 0.001 TYR A 107 ARG 0.007 0.000 ARG C 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5286.64 seconds wall clock time: 91 minutes 9.88 seconds (5469.88 seconds total)