Starting phenix.real_space_refine on Fri Aug 22 21:02:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8itm_35707/08_2025/8itm_35707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8itm_35707/08_2025/8itm_35707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8itm_35707/08_2025/8itm_35707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8itm_35707/08_2025/8itm_35707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8itm_35707/08_2025/8itm_35707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8itm_35707/08_2025/8itm_35707.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.003 sd= 0.092 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5008 2.51 5 N 1410 2.21 5 O 1440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7905 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2153 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 6, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 7, 'PHE:plan': 5, 'ASP:plan': 2, 'ARG:plan': 7, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 111 Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1868 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2552 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "G" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 382 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "N" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 950 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.03, per 1000 atoms: 0.26 Number of scatterers: 7905 At special positions: 0 Unit cell: (76.041, 101.745, 127.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1440 8.00 N 1410 7.00 C 5008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 155 " - pdb=" SG CYS R 225 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 0.67 Conformation dependent library (CDL) restraints added in 432.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 11 sheets defined 43.1% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'R' and resid 63 through 101 Processing helix chain 'R' and resid 106 through 133 removed outlier: 3.723A pdb=" N LEU R 127 " --> pdb=" O ALA R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 186 removed outlier: 3.935A pdb=" N TYR R 170 " --> pdb=" O VAL R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 194 through 220 Proline residue: R 206 - end of helix Proline residue: R 212 - end of helix Processing helix chain 'R' and resid 231 through 268 removed outlier: 3.856A pdb=" N ILE R 237 " --> pdb=" O ALA R 233 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE R 238 " --> pdb=" O ILE R 234 " (cutoff:3.500A) Proline residue: R 241 - end of helix removed outlier: 3.783A pdb=" N ARG R 267 " --> pdb=" O LYS R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 290 removed outlier: 3.910A pdb=" N ARG R 277 " --> pdb=" O ASP R 273 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU R 278 " --> pdb=" O TYR R 274 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 290 through 296 Processing helix chain 'R' and resid 306 through 331 removed outlier: 4.265A pdb=" N PHE R 310 " --> pdb=" O GLY R 306 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE R 317 " --> pdb=" O LEU R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 354 Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.757A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.694A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.529A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.837A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.318A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.573A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 209 removed outlier: 3.623A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 209 removed outlier: 6.615A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.274A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.904A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.567A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.526A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.597A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.793A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.584A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.741A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1242 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: 1.32 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2619 1.34 - 1.46: 1947 1.46 - 1.58: 3429 1.58 - 1.70: 0 1.70 - 1.83: 65 Bond restraints: 8060 Sorted by residual: bond pdb=" C VAL R 286 " pdb=" N PRO R 287 " ideal model delta sigma weight residual 1.335 1.354 -0.020 1.28e-02 6.10e+03 2.37e+00 bond pdb=" CA GLU R 301 " pdb=" C GLU R 301 " ideal model delta sigma weight residual 1.525 1.508 0.017 1.29e-02 6.01e+03 1.79e+00 bond pdb=" C ALA R 297 " pdb=" O ALA R 297 " ideal model delta sigma weight residual 1.244 1.231 0.012 1.00e-02 1.00e+04 1.54e+00 bond pdb=" CA THR R 300 " pdb=" C THR R 300 " ideal model delta sigma weight residual 1.528 1.512 0.015 1.33e-02 5.65e+03 1.33e+00 bond pdb=" CB ASN R 249 " pdb=" CG ASN R 249 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.28e+00 ... (remaining 8055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 10685 1.62 - 3.23: 208 3.23 - 4.85: 36 4.85 - 6.46: 14 6.46 - 8.08: 5 Bond angle restraints: 10948 Sorted by residual: angle pdb=" C VAL R 286 " pdb=" CA VAL R 286 " pdb=" CB VAL R 286 " ideal model delta sigma weight residual 113.70 110.17 3.53 9.50e-01 1.11e+00 1.38e+01 angle pdb=" N GLU R 316 " pdb=" CA GLU R 316 " pdb=" CB GLU R 316 " ideal model delta sigma weight residual 110.16 115.59 -5.43 1.48e+00 4.57e-01 1.34e+01 angle pdb=" N GLU R 301 " pdb=" CA GLU R 301 " pdb=" C GLU R 301 " ideal model delta sigma weight residual 112.04 107.15 4.89 1.44e+00 4.82e-01 1.15e+01 angle pdb=" CA ALA R 297 " pdb=" C ALA R 297 " pdb=" N PRO R 298 " ideal model delta sigma weight residual 120.77 117.70 3.07 9.70e-01 1.06e+00 1.00e+01 angle pdb=" N ARG R 305 " pdb=" CA ARG R 305 " pdb=" C ARG R 305 " ideal model delta sigma weight residual 109.76 114.66 -4.90 1.59e+00 3.96e-01 9.50e+00 ... (remaining 10943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4283 17.46 - 34.92: 401 34.92 - 52.37: 73 52.37 - 69.83: 9 69.83 - 87.29: 8 Dihedral angle restraints: 4774 sinusoidal: 1770 harmonic: 3004 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -17.74 -68.26 1 1.00e+01 1.00e-02 6.04e+01 dihedral pdb=" CB CYS R 155 " pdb=" SG CYS R 155 " pdb=" SG CYS R 225 " pdb=" CB CYS R 225 " ideal model delta sinusoidal sigma weight residual 93.00 45.78 47.22 1 1.00e+01 1.00e-02 3.08e+01 dihedral pdb=" CA ALA B 60 " pdb=" C ALA B 60 " pdb=" N MET B 61 " pdb=" CA MET B 61 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 4771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 719 0.029 - 0.058: 352 0.058 - 0.087: 110 0.087 - 0.117: 62 0.117 - 0.146: 18 Chirality restraints: 1261 Sorted by residual: chirality pdb=" CG LEU B 14 " pdb=" CB LEU B 14 " pdb=" CD1 LEU B 14 " pdb=" CD2 LEU B 14 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CG LEU R 183 " pdb=" CB LEU R 183 " pdb=" CD1 LEU R 183 " pdb=" CD2 LEU R 183 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE A 207 " pdb=" N ILE A 207 " pdb=" C ILE A 207 " pdb=" CB ILE A 207 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1258 not shown) Planarity restraints: 1397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 327 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C VAL R 327 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL R 327 " 0.012 2.00e-02 2.50e+03 pdb=" N SER R 328 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 312 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C LYS R 312 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS R 312 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU R 313 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.013 2.00e-02 2.50e+03 1.11e-02 2.48e+00 pdb=" CG TYR B 59 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.001 2.00e-02 2.50e+03 ... (remaining 1394 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1135 2.75 - 3.29: 7700 3.29 - 3.83: 13201 3.83 - 4.36: 14907 4.36 - 4.90: 26941 Nonbonded interactions: 63884 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.218 3.040 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.234 3.040 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.257 3.120 nonbonded pdb=" NZ LYS B 57 " pdb=" OH TYR B 59 " model vdw 2.260 3.120 nonbonded pdb=" OG SER R 118 " pdb=" OD1 ASN R 169 " model vdw 2.270 3.040 ... (remaining 63879 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.130 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 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 0.037 8063 Z= 0.180 Angle : 0.610 8.076 10954 Z= 0.347 Chirality : 0.042 0.146 1261 Planarity : 0.003 0.031 1397 Dihedral : 14.137 87.289 2823 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.27), residues: 1019 helix: 1.81 (0.26), residues: 422 sheet: -0.77 (0.35), residues: 226 loop : -1.55 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 20 TYR 0.027 0.002 TYR B 59 PHE 0.016 0.001 PHE R 310 TRP 0.008 0.001 TRP A 234 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8060) covalent geometry : angle 0.60937 (10948) SS BOND : bond 0.00163 ( 3) SS BOND : angle 1.08323 ( 6) hydrogen bonds : bond 0.14289 ( 426) hydrogen bonds : angle 6.51590 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: R 191 GLU cc_start: 0.5105 (pp20) cc_final: 0.3897 (pm20) REVERT: R 234 ILE cc_start: 0.7892 (mm) cc_final: 0.7567 (pt) REVERT: A 31 GLN cc_start: 0.7830 (tp-100) cc_final: 0.7358 (tp-100) REVERT: A 381 ASP cc_start: 0.8420 (t0) cc_final: 0.8156 (t0) REVERT: B 243 THR cc_start: 0.8781 (p) cc_final: 0.8521 (p) REVERT: B 262 MET cc_start: 0.7858 (ppp) cc_final: 0.7612 (ppp) REVERT: B 264 TYR cc_start: 0.8516 (m-80) cc_final: 0.8007 (m-80) REVERT: B 291 ASP cc_start: 0.7774 (p0) cc_final: 0.7551 (p0) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1122 time to fit residues: 20.5886 Evaluate side-chains 122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 109 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.183939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.141918 restraints weight = 9275.648| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.78 r_work: 0.3298 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8063 Z= 0.127 Angle : 0.546 6.527 10954 Z= 0.288 Chirality : 0.041 0.141 1261 Planarity : 0.003 0.029 1397 Dihedral : 4.046 18.542 1130 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.25 % Allowed : 8.84 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.27), residues: 1019 helix: 2.08 (0.26), residues: 424 sheet: -0.60 (0.34), residues: 213 loop : -1.50 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.028 0.001 TYR R 80 PHE 0.016 0.001 PHE R 310 TRP 0.014 0.001 TRP B 297 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8060) covalent geometry : angle 0.54574 (10948) SS BOND : bond 0.00051 ( 3) SS BOND : angle 1.09572 ( 6) hydrogen bonds : bond 0.03881 ( 426) hydrogen bonds : angle 4.72074 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6744 (mm) REVERT: R 191 GLU cc_start: 0.4882 (pp20) cc_final: 0.3979 (pm20) REVERT: R 234 ILE cc_start: 0.7918 (mm) cc_final: 0.7539 (pt) REVERT: A 31 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7651 (tp-100) REVERT: A 381 ASP cc_start: 0.8772 (t0) cc_final: 0.8387 (t0) REVERT: A 386 MET cc_start: 0.8279 (tmm) cc_final: 0.8047 (tmm) REVERT: B 264 TYR cc_start: 0.8672 (m-80) cc_final: 0.8291 (m-80) REVERT: N 73 ASP cc_start: 0.7717 (t70) cc_final: 0.7507 (t0) REVERT: N 82 GLN cc_start: 0.8331 (tp40) cc_final: 0.7927 (tp-100) outliers start: 10 outliers final: 5 residues processed: 137 average time/residue: 0.0874 time to fit residues: 16.3253 Evaluate side-chains 125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** 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 = 0.4076 r_free = 0.4076 target = 0.183577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.141444 restraints weight = 9213.347| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.81 r_work: 0.3296 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8063 Z= 0.136 Angle : 0.522 6.526 10954 Z= 0.275 Chirality : 0.041 0.146 1261 Planarity : 0.003 0.032 1397 Dihedral : 3.968 17.929 1130 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.62 % Allowed : 11.33 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.27), residues: 1019 helix: 2.09 (0.26), residues: 428 sheet: -0.47 (0.34), residues: 215 loop : -1.59 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.027 0.001 TYR R 80 PHE 0.017 0.001 PHE R 310 TRP 0.012 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8060) covalent geometry : angle 0.52132 (10948) SS BOND : bond 0.00109 ( 3) SS BOND : angle 0.99382 ( 6) hydrogen bonds : bond 0.03780 ( 426) hydrogen bonds : angle 4.39832 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6745 (mm) REVERT: R 191 GLU cc_start: 0.4841 (pp20) cc_final: 0.3924 (pm20) REVERT: R 234 ILE cc_start: 0.7921 (mm) cc_final: 0.7556 (pt) REVERT: R 331 TYR cc_start: 0.5969 (t80) cc_final: 0.5759 (t80) REVERT: A 31 GLN cc_start: 0.8172 (tp-100) cc_final: 0.7652 (tp-100) REVERT: A 381 ASP cc_start: 0.8801 (t70) cc_final: 0.8535 (t0) REVERT: B 264 TYR cc_start: 0.8678 (m-80) cc_final: 0.8239 (m-80) outliers start: 13 outliers final: 8 residues processed: 135 average time/residue: 0.0929 time to fit residues: 17.0062 Evaluate side-chains 132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 100 optimal weight: 0.0870 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.184440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.143141 restraints weight = 9401.527| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.81 r_work: 0.3293 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8063 Z= 0.143 Angle : 0.516 6.422 10954 Z= 0.271 Chirality : 0.041 0.168 1261 Planarity : 0.003 0.030 1397 Dihedral : 3.933 18.231 1130 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.86 % Allowed : 12.45 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.27), residues: 1019 helix: 2.09 (0.26), residues: 428 sheet: -0.39 (0.34), residues: 209 loop : -1.67 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.025 0.001 TYR R 80 PHE 0.018 0.001 PHE R 310 TRP 0.011 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8060) covalent geometry : angle 0.51562 (10948) SS BOND : bond 0.00117 ( 3) SS BOND : angle 0.93280 ( 6) hydrogen bonds : bond 0.03699 ( 426) hydrogen bonds : angle 4.23010 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6898 (mm) REVERT: R 191 GLU cc_start: 0.4825 (pp20) cc_final: 0.3964 (pm20) REVERT: R 234 ILE cc_start: 0.7980 (mm) cc_final: 0.7619 (pt) REVERT: A 31 GLN cc_start: 0.8179 (tp-100) cc_final: 0.7687 (tp-100) REVERT: A 381 ASP cc_start: 0.8812 (t70) cc_final: 0.8549 (t0) REVERT: A 386 MET cc_start: 0.8227 (tmm) cc_final: 0.8007 (tmm) REVERT: B 262 MET cc_start: 0.8270 (ppp) cc_final: 0.7979 (ptm) REVERT: B 264 TYR cc_start: 0.8689 (m-80) cc_final: 0.8179 (m-80) REVERT: N 32 TYR cc_start: 0.8829 (m-80) cc_final: 0.8489 (m-80) outliers start: 23 outliers final: 12 residues processed: 142 average time/residue: 0.0862 time to fit residues: 16.5724 Evaluate side-chains 136 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 75 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.183934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142214 restraints weight = 9289.922| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.87 r_work: 0.3297 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8063 Z= 0.126 Angle : 0.520 7.306 10954 Z= 0.267 Chirality : 0.041 0.186 1261 Planarity : 0.003 0.030 1397 Dihedral : 3.871 17.511 1130 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.86 % Allowed : 14.20 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.27), residues: 1019 helix: 2.28 (0.26), residues: 421 sheet: -0.28 (0.34), residues: 209 loop : -1.60 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.027 0.001 TYR R 80 PHE 0.016 0.001 PHE R 310 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8060) covalent geometry : angle 0.51965 (10948) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.84967 ( 6) hydrogen bonds : bond 0.03533 ( 426) hydrogen bonds : angle 4.10745 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6955 (mm) REVERT: R 191 GLU cc_start: 0.4835 (pp20) cc_final: 0.3987 (pm20) REVERT: R 234 ILE cc_start: 0.7989 (mm) cc_final: 0.7630 (pt) REVERT: A 31 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7721 (tp-100) REVERT: A 381 ASP cc_start: 0.8795 (t70) cc_final: 0.8507 (t0) REVERT: B 217 MET cc_start: 0.8244 (pmm) cc_final: 0.8032 (pmm) REVERT: B 262 MET cc_start: 0.8273 (ppp) cc_final: 0.8023 (ptm) REVERT: B 264 TYR cc_start: 0.8634 (m-80) cc_final: 0.8118 (m-80) REVERT: N 32 TYR cc_start: 0.8796 (m-80) cc_final: 0.8512 (m-80) outliers start: 23 outliers final: 16 residues processed: 142 average time/residue: 0.0863 time to fit residues: 16.6314 Evaluate side-chains 140 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 75 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.183288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141405 restraints weight = 9278.379| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.68 r_work: 0.3283 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8063 Z= 0.140 Angle : 0.516 6.959 10954 Z= 0.267 Chirality : 0.041 0.173 1261 Planarity : 0.003 0.029 1397 Dihedral : 3.878 18.018 1130 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.86 % Allowed : 15.69 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.27), residues: 1019 helix: 2.24 (0.26), residues: 422 sheet: -0.31 (0.33), residues: 215 loop : -1.54 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.025 0.001 TYR R 80 PHE 0.015 0.001 PHE R 310 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8060) covalent geometry : angle 0.51583 (10948) SS BOND : bond 0.00170 ( 3) SS BOND : angle 0.81183 ( 6) hydrogen bonds : bond 0.03581 ( 426) hydrogen bonds : angle 4.07440 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6995 (mm) REVERT: R 191 GLU cc_start: 0.4838 (pp20) cc_final: 0.3921 (pm20) REVERT: R 234 ILE cc_start: 0.7985 (mm) cc_final: 0.7635 (pt) REVERT: R 331 TYR cc_start: 0.6178 (OUTLIER) cc_final: 0.5585 (t80) REVERT: A 31 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7746 (tp-100) REVERT: A 381 ASP cc_start: 0.8794 (t70) cc_final: 0.8548 (t0) REVERT: B 262 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7973 (ptm) REVERT: B 264 TYR cc_start: 0.8657 (m-80) cc_final: 0.8151 (m-80) REVERT: N 32 TYR cc_start: 0.8881 (m-80) cc_final: 0.8431 (m-80) REVERT: N 120 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7243 (mm110) outliers start: 23 outliers final: 16 residues processed: 131 average time/residue: 0.0857 time to fit residues: 15.4623 Evaluate side-chains 138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 331 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.184000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.142328 restraints weight = 9317.601| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.67 r_work: 0.3300 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8063 Z= 0.124 Angle : 0.516 9.366 10954 Z= 0.265 Chirality : 0.040 0.174 1261 Planarity : 0.003 0.029 1397 Dihedral : 3.824 17.290 1130 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.24 % Allowed : 15.69 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.27), residues: 1019 helix: 2.29 (0.26), residues: 422 sheet: -0.15 (0.34), residues: 209 loop : -1.52 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 20 TYR 0.024 0.001 TYR R 80 PHE 0.015 0.001 PHE R 310 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8060) covalent geometry : angle 0.51540 (10948) SS BOND : bond 0.00111 ( 3) SS BOND : angle 0.85044 ( 6) hydrogen bonds : bond 0.03544 ( 426) hydrogen bonds : angle 4.02393 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6975 (mm) REVERT: R 191 GLU cc_start: 0.4732 (pp20) cc_final: 0.3787 (pm20) REVERT: R 234 ILE cc_start: 0.7962 (mm) cc_final: 0.7607 (pt) REVERT: R 331 TYR cc_start: 0.6143 (OUTLIER) cc_final: 0.5574 (t80) REVERT: A 31 GLN cc_start: 0.8238 (tp-100) cc_final: 0.7752 (tp-100) REVERT: A 60 MET cc_start: 0.5569 (ptt) cc_final: 0.5288 (ptt) REVERT: A 381 ASP cc_start: 0.8800 (t70) cc_final: 0.8568 (t0) REVERT: B 234 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.7902 (t80) REVERT: B 262 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7931 (ptm) REVERT: B 264 TYR cc_start: 0.8638 (m-80) cc_final: 0.8146 (m-80) REVERT: N 31 ASN cc_start: 0.9062 (m-40) cc_final: 0.8847 (m-40) REVERT: N 32 TYR cc_start: 0.8843 (m-80) cc_final: 0.8417 (m-80) outliers start: 26 outliers final: 17 residues processed: 140 average time/residue: 0.0824 time to fit residues: 15.7976 Evaluate side-chains 144 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 331 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 56 optimal weight: 0.6980 chunk 100 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.183603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141682 restraints weight = 9282.361| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.59 r_work: 0.3307 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8063 Z= 0.128 Angle : 0.516 9.184 10954 Z= 0.265 Chirality : 0.041 0.172 1261 Planarity : 0.003 0.029 1397 Dihedral : 3.827 17.237 1130 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.86 % Allowed : 16.31 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.27), residues: 1019 helix: 2.30 (0.26), residues: 422 sheet: -0.14 (0.34), residues: 209 loop : -1.52 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 20 TYR 0.024 0.001 TYR R 80 PHE 0.015 0.001 PHE R 310 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8060) covalent geometry : angle 0.51536 (10948) SS BOND : bond 0.00166 ( 3) SS BOND : angle 0.79812 ( 6) hydrogen bonds : bond 0.03533 ( 426) hydrogen bonds : angle 4.00626 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6989 (mm) REVERT: R 191 GLU cc_start: 0.4740 (pp20) cc_final: 0.3808 (pm20) REVERT: R 234 ILE cc_start: 0.7953 (mm) cc_final: 0.7592 (pt) REVERT: R 331 TYR cc_start: 0.6243 (OUTLIER) cc_final: 0.5617 (t80) REVERT: A 31 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7744 (tp-100) REVERT: A 60 MET cc_start: 0.5595 (ptt) cc_final: 0.5352 (ptt) REVERT: A 381 ASP cc_start: 0.8786 (t70) cc_final: 0.8552 (t0) REVERT: B 212 ASP cc_start: 0.7697 (p0) cc_final: 0.7409 (p0) REVERT: B 234 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.7979 (t80) REVERT: B 262 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7954 (ptm) REVERT: B 264 TYR cc_start: 0.8656 (m-80) cc_final: 0.8169 (m-80) REVERT: N 6 GLU cc_start: 0.7717 (mp0) cc_final: 0.7414 (mp0) REVERT: N 31 ASN cc_start: 0.9073 (m-40) cc_final: 0.8844 (m-40) REVERT: N 32 TYR cc_start: 0.8834 (m-80) cc_final: 0.8392 (m-80) outliers start: 23 outliers final: 18 residues processed: 138 average time/residue: 0.0757 time to fit residues: 14.4582 Evaluate side-chains 146 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 331 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 0.0770 chunk 47 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.183691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141722 restraints weight = 9190.161| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.58 r_work: 0.3312 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8063 Z= 0.122 Angle : 0.513 8.869 10954 Z= 0.264 Chirality : 0.040 0.170 1261 Planarity : 0.003 0.030 1397 Dihedral : 3.803 16.888 1130 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.99 % Allowed : 16.69 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.27), residues: 1019 helix: 2.33 (0.26), residues: 422 sheet: -0.26 (0.33), residues: 216 loop : -1.44 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 20 TYR 0.026 0.001 TYR R 80 PHE 0.014 0.001 PHE R 310 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8060) covalent geometry : angle 0.51297 (10948) SS BOND : bond 0.00175 ( 3) SS BOND : angle 0.77558 ( 6) hydrogen bonds : bond 0.03485 ( 426) hydrogen bonds : angle 3.97823 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: R 191 GLU cc_start: 0.4697 (pp20) cc_final: 0.3798 (pm20) REVERT: R 234 ILE cc_start: 0.7934 (mm) cc_final: 0.7568 (pt) REVERT: R 331 TYR cc_start: 0.6254 (OUTLIER) cc_final: 0.5607 (t80) REVERT: A 31 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7736 (tp-100) REVERT: A 60 MET cc_start: 0.5540 (ptt) cc_final: 0.5319 (ptt) REVERT: A 381 ASP cc_start: 0.8815 (t70) cc_final: 0.8557 (t0) REVERT: B 212 ASP cc_start: 0.7672 (p0) cc_final: 0.7399 (p0) REVERT: B 234 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8010 (t80) REVERT: B 262 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7920 (ptp) REVERT: B 264 TYR cc_start: 0.8643 (m-80) cc_final: 0.8166 (m-80) REVERT: N 6 GLU cc_start: 0.7716 (mp0) cc_final: 0.7434 (mp0) REVERT: N 31 ASN cc_start: 0.9077 (m-40) cc_final: 0.8847 (m-40) REVERT: N 32 TYR cc_start: 0.8827 (m-80) cc_final: 0.8408 (m-80) outliers start: 24 outliers final: 18 residues processed: 140 average time/residue: 0.0900 time to fit residues: 17.4350 Evaluate side-chains 146 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 331 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.183553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.141022 restraints weight = 9221.990| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.69 r_work: 0.3292 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8063 Z= 0.139 Angle : 0.551 8.855 10954 Z= 0.279 Chirality : 0.041 0.221 1261 Planarity : 0.003 0.033 1397 Dihedral : 3.835 17.342 1130 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.74 % Allowed : 17.43 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.27), residues: 1019 helix: 2.31 (0.26), residues: 422 sheet: -0.15 (0.34), residues: 205 loop : -1.50 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 20 TYR 0.026 0.001 TYR R 80 PHE 0.015 0.001 PHE R 310 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8060) covalent geometry : angle 0.55081 (10948) SS BOND : bond 0.00176 ( 3) SS BOND : angle 0.81646 ( 6) hydrogen bonds : bond 0.03580 ( 426) hydrogen bonds : angle 3.97571 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6917 (mm) REVERT: R 191 GLU cc_start: 0.4700 (pp20) cc_final: 0.3789 (pm20) REVERT: R 234 ILE cc_start: 0.7951 (mm) cc_final: 0.7586 (pt) REVERT: R 331 TYR cc_start: 0.6292 (OUTLIER) cc_final: 0.5569 (t80) REVERT: A 31 GLN cc_start: 0.8240 (tp-100) cc_final: 0.7744 (tp-100) REVERT: A 60 MET cc_start: 0.5604 (ptt) cc_final: 0.5127 (ptt) REVERT: A 381 ASP cc_start: 0.8820 (t70) cc_final: 0.8561 (t0) REVERT: B 234 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8048 (t80) REVERT: B 262 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7966 (ptm) REVERT: B 264 TYR cc_start: 0.8670 (m-80) cc_final: 0.8173 (m-80) REVERT: N 6 GLU cc_start: 0.7746 (mp0) cc_final: 0.7463 (mp0) REVERT: N 31 ASN cc_start: 0.9094 (m-40) cc_final: 0.8856 (m-40) REVERT: N 32 TYR cc_start: 0.8833 (m-80) cc_final: 0.8382 (m-80) outliers start: 22 outliers final: 18 residues processed: 135 average time/residue: 0.0779 time to fit residues: 14.6586 Evaluate side-chains 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 331 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.183958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142086 restraints weight = 9233.549| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.63 r_work: 0.3307 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8063 Z= 0.129 Angle : 0.547 10.513 10954 Z= 0.276 Chirality : 0.041 0.201 1261 Planarity : 0.003 0.035 1397 Dihedral : 3.820 17.167 1130 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.74 % Allowed : 17.56 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.27), residues: 1019 helix: 2.36 (0.26), residues: 422 sheet: -0.21 (0.34), residues: 211 loop : -1.43 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 20 TYR 0.026 0.001 TYR R 80 PHE 0.024 0.001 PHE R 195 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8060) covalent geometry : angle 0.54667 (10948) SS BOND : bond 0.00176 ( 3) SS BOND : angle 0.77950 ( 6) hydrogen bonds : bond 0.03529 ( 426) hydrogen bonds : angle 3.98540 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1853.80 seconds wall clock time: 32 minutes 29.08 seconds (1949.08 seconds total)