Starting phenix.real_space_refine on Sat Dec 28 02:09:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wog_37686/12_2024/8wog_37686_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wog_37686/12_2024/8wog_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_37686/12_2024/8wog_37686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wog_37686/12_2024/8wog_37686.map" model { file = "/net/cci-nas-00/data/ceres_data/8wog_37686/12_2024/8wog_37686_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wog_37686/12_2024/8wog_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-5532/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: 4.72, per 1000 atoms: 0.64 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: 1.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.80 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: 2.04 Time building geometry restraints manager: 2.11 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: 2.110 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.900 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.210 ------------------------------------------------------------------------------- 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 : 0.850 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: 1.2721 time to fit residues: 163.8484 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 : 0.753 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.863 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6551 (mmp-170) REVERT: A 90 TYR cc_start: 0.6049 (m-80) cc_final: 0.5810 (m-80) REVERT: A 189 MET cc_start: 0.8047 (tpt) cc_final: 0.7797 (mmm) REVERT: A 263 TRP cc_start: 0.6544 (OUTLIER) cc_final: 0.6256 (t-100) REVERT: D 188 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8337 (mmm) REVERT: D 258 ASP cc_start: 0.8388 (t0) cc_final: 0.8029 (t0) outliers start: 46 outliers final: 22 residues processed: 128 average time/residue: 1.2446 time to fit residues: 168.5289 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 : 0.819 ------------------------------------------------------------------------------- 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 45 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 56 optimal weight: 0.0030 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 D 340 ASN E 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0927 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= 0.153 Angle : 0.396 4.202 10200 Z= 0.220 Chirality : 0.039 0.131 1166 Planarity : 0.003 0.035 1288 Dihedral : 5.206 56.830 1025 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.93 % Allowed : 20.72 % 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: 1.28 (0.29), residues: 916 helix: 2.85 (0.27), residues: 394 sheet: 0.21 (0.39), residues: 171 loop : -1.24 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 0.005 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 140 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6501 (mmp-170) REVERT: A 90 TYR cc_start: 0.6143 (m-80) cc_final: 0.5871 (m-80) REVERT: A 130 GLU cc_start: 0.8492 (pm20) cc_final: 0.8205 (pm20) REVERT: A 189 MET cc_start: 0.8000 (tpt) cc_final: 0.7755 (mmm) REVERT: C 32 ARG cc_start: 0.8254 (mtm-85) cc_final: 0.7770 (mtt-85) REVERT: D 217 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8496 (ptt) REVERT: D 258 ASP cc_start: 0.8414 (t0) cc_final: 0.8038 (t0) outliers start: 40 outliers final: 21 residues processed: 126 average time/residue: 1.2554 time to fit residues: 167.4232 Evaluate side-chains 121 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 234 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain C residue 20 ASP 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 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 217 MET Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 270 ILE 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 62 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 313 ASN D 340 ASN E 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 0.006 0.039 7531 Z= 0.403 Angle : 0.551 7.825 10200 Z= 0.296 Chirality : 0.044 0.142 1166 Planarity : 0.004 0.039 1288 Dihedral : 5.476 59.633 1019 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 7.03 % Allowed : 18.87 % Favored : 74.11 % 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: 0.77 (0.28), residues: 916 helix: 2.41 (0.27), residues: 395 sheet: -0.11 (0.39), residues: 168 loop : -1.46 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 263 HIS 0.006 0.001 HIS D 183 PHE 0.017 0.002 PHE A 115 TYR 0.019 0.001 TYR A 107 ARG 0.006 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 153 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 96 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8095 (t80) REVERT: A 81 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6520 (mmp-170) REVERT: A 263 TRP cc_start: 0.6310 (OUTLIER) cc_final: 0.5981 (t-100) REVERT: C 33 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8289 (mt-10) REVERT: C 242 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6929 (mtt180) REVERT: D 138 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8810 (tt0) REVERT: D 188 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8405 (mmm) REVERT: D 189 SER cc_start: 0.9199 (OUTLIER) cc_final: 0.8970 (p) REVERT: D 198 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8954 (mp) REVERT: D 214 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.6877 (mpp-170) REVERT: D 217 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8582 (ptt) REVERT: D 258 ASP cc_start: 0.8431 (t0) cc_final: 0.8229 (t0) outliers start: 57 outliers final: 28 residues processed: 132 average time/residue: 1.2086 time to fit residues: 168.7391 Evaluate side-chains 131 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 263 TRP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 33 GLU 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 102 THR Chi-restraints excluded: chain D residue 138 GLU 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 217 MET Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 269 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.0030 chunk 1 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 0.1980 chunk 78 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1221 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= 0.143 Angle : 0.402 5.716 10200 Z= 0.222 Chirality : 0.039 0.131 1166 Planarity : 0.003 0.035 1288 Dihedral : 5.073 58.390 1019 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.55 % Allowed : 20.72 % Favored : 73.74 % 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: 1.06 (0.29), residues: 916 helix: 2.69 (0.27), residues: 399 sheet: -0.06 (0.39), residues: 167 loop : -1.33 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 0.007 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 139 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 94 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6544 (mmp-170) REVERT: A 130 GLU cc_start: 0.8468 (pm20) cc_final: 0.8192 (pm20) REVERT: A 265 GLN cc_start: 0.5877 (OUTLIER) cc_final: 0.5537 (mp10) REVERT: C 32 ARG cc_start: 0.8211 (mtm-85) cc_final: 0.7675 (mtt-85) REVERT: C 33 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: D 188 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8352 (mmm) REVERT: D 189 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8942 (p) outliers start: 45 outliers final: 27 residues processed: 121 average time/residue: 1.2552 time to fit residues: 160.3638 Evaluate side-chains 124 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 171 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 265 GLN 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 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 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 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 270 ILE Chi-restraints excluded: chain D residue 292 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 88 optimal weight: 0.0070 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 7531 Z= 0.366 Angle : 0.517 7.188 10200 Z= 0.278 Chirality : 0.043 0.144 1166 Planarity : 0.003 0.037 1288 Dihedral : 5.383 59.744 1018 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.92 % Allowed : 21.33 % Favored : 72.75 % 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: 0.79 (0.28), residues: 916 helix: 2.43 (0.27), residues: 396 sheet: -0.14 (0.39), residues: 167 loop : -1.43 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 82 HIS 0.007 0.001 HIS D 183 PHE 0.017 0.002 PHE D 292 TYR 0.018 0.001 TYR A 107 ARG 0.008 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: 48 poor density : 94 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.8025 (t80) REVERT: A 81 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6522 (mmp-170) REVERT: A 263 TRP cc_start: 0.6106 (OUTLIER) cc_final: 0.5698 (t-100) REVERT: A 265 GLN cc_start: 0.5871 (OUTLIER) cc_final: 0.5514 (mp10) REVERT: C 32 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7747 (mtt-85) REVERT: C 33 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8274 (mt-10) REVERT: C 298 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6866 (tp30) REVERT: D 82 TRP cc_start: 0.9285 (OUTLIER) cc_final: 0.9009 (m100) REVERT: D 188 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8405 (mmm) REVERT: D 189 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8977 (p) REVERT: D 214 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.6890 (mpp-170) REVERT: D 254 ASP cc_start: 0.8357 (t0) cc_final: 0.8026 (t0) outliers start: 48 outliers final: 29 residues processed: 125 average time/residue: 1.2211 time to fit residues: 161.2589 Evaluate side-chains 130 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 263 TRP Chi-restraints excluded: chain A residue 265 GLN 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7531 Z= 0.158 Angle : 0.409 6.506 10200 Z= 0.225 Chirality : 0.039 0.133 1166 Planarity : 0.003 0.035 1288 Dihedral : 5.092 59.079 1018 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.81 % Allowed : 22.56 % 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: 1.08 (0.29), residues: 916 helix: 2.76 (0.27), residues: 394 sheet: -0.08 (0.39), residues: 166 loop : -1.32 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 82 HIS 0.006 0.001 HIS D 183 PHE 0.010 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: 39 poor density : 94 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6474 (mmp-170) REVERT: A 265 GLN cc_start: 0.5962 (OUTLIER) cc_final: 0.5554 (mp10) REVERT: C 32 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7669 (mtt-85) REVERT: C 33 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: D 189 SER cc_start: 0.9170 (OUTLIER) cc_final: 0.8967 (p) REVERT: D 254 ASP cc_start: 0.8292 (t0) cc_final: 0.7902 (t0) outliers start: 39 outliers final: 30 residues processed: 117 average time/residue: 1.2947 time to fit residues: 159.8037 Evaluate side-chains 123 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 155 LEU 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 236 MET Chi-restraints excluded: chain A residue 265 GLN 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 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 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 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 26 optimal weight: 0.0980 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7531 Z= 0.152 Angle : 0.409 7.076 10200 Z= 0.224 Chirality : 0.039 0.134 1166 Planarity : 0.003 0.034 1288 Dihedral : 4.996 59.481 1018 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.69 % Allowed : 22.81 % 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: 1.21 (0.29), residues: 916 helix: 2.87 (0.27), residues: 394 sheet: -0.06 (0.39), residues: 166 loop : -1.23 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 82 HIS 0.006 0.001 HIS D 183 PHE 0.009 0.001 PHE C 189 TYR 0.013 0.001 TYR A 107 ARG 0.009 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 131 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6506 (mmp-170) REVERT: A 265 GLN cc_start: 0.5926 (OUTLIER) cc_final: 0.5520 (mp10) REVERT: C 33 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8215 (mt-10) outliers start: 38 outliers final: 27 residues processed: 116 average time/residue: 1.2695 time to fit residues: 155.5747 Evaluate side-chains 122 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 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 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 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 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 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 317 CYS 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 81 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 7531 Z= 0.308 Angle : 0.497 7.411 10200 Z= 0.267 Chirality : 0.042 0.137 1166 Planarity : 0.003 0.035 1288 Dihedral : 5.310 59.744 1018 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.93 % Allowed : 22.69 % 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: 0.97 (0.29), residues: 916 helix: 2.63 (0.27), residues: 394 sheet: -0.13 (0.40), residues: 166 loop : -1.32 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 263 HIS 0.007 0.001 HIS D 183 PHE 0.016 0.002 PHE D 292 TYR 0.017 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 132 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.7768 (t80) REVERT: A 81 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6445 (mmp-170) REVERT: A 265 GLN cc_start: 0.6006 (OUTLIER) cc_final: 0.5539 (mp10) REVERT: C 33 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8248 (mt-10) REVERT: D 214 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.6896 (mpp-170) outliers start: 40 outliers final: 30 residues processed: 118 average time/residue: 1.2530 time to fit residues: 156.1138 Evaluate side-chains 125 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 152 LEU 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 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 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 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 183 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7531 Z= 0.169 Angle : 0.426 7.585 10200 Z= 0.232 Chirality : 0.039 0.134 1166 Planarity : 0.003 0.034 1288 Dihedral : 5.107 59.974 1018 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.07 % Allowed : 23.30 % 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: 1.14 (0.29), residues: 916 helix: 2.81 (0.27), residues: 394 sheet: -0.14 (0.39), residues: 166 loop : -1.24 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 82 HIS 0.006 0.001 HIS D 183 PHE 0.010 0.001 PHE D 292 TYR 0.012 0.001 TYR A 107 ARG 0.009 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 124 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 15 LEU cc_start: 0.8173 (tt) cc_final: 0.7948 (pp) REVERT: A 81 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6507 (mmp-170) REVERT: A 265 GLN cc_start: 0.5919 (OUTLIER) cc_final: 0.5493 (mp10) REVERT: D 254 ASP cc_start: 0.8379 (t0) cc_final: 0.7953 (t0) outliers start: 33 outliers final: 30 residues processed: 112 average time/residue: 1.2684 time to fit residues: 149.8302 Evaluate side-chains 122 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain A residue 171 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 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 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 183 HIS 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 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 66 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.157674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107888 restraints weight = 8044.841| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.72 r_work: 0.3037 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7531 Z= 0.175 Angle : 0.427 7.775 10200 Z= 0.231 Chirality : 0.039 0.132 1166 Planarity : 0.003 0.035 1288 Dihedral : 5.047 59.433 1018 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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: 1.18 (0.29), residues: 916 helix: 2.86 (0.27), residues: 394 sheet: -0.13 (0.39), residues: 166 loop : -1.22 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 82 HIS 0.006 0.001 HIS D 183 PHE 0.011 0.001 PHE D 292 TYR 0.013 0.001 TYR A 107 ARG 0.009 0.000 ARG C 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3126.07 seconds wall clock time: 56 minutes 35.88 seconds (3395.88 seconds total)