Starting phenix.real_space_refine on Wed Feb 12 12:51:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8itm_35707/02_2025/8itm_35707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8itm_35707/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8itm_35707/02_2025/8itm_35707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8itm_35707/02_2025/8itm_35707.map" model { file = "/net/cci-nas-00/data/ceres_data/8itm_35707/02_2025/8itm_35707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8itm_35707/02_2025/8itm_35707.cif" } resolution = 3.13 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= -0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 7} 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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 8} 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, 'GLU:plan': 2, 'ARG: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: 4.47, per 1000 atoms: 0.57 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: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.85 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: 2.23 Time building geometry restraints manager: 2.29 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: 1.510 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.980 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.710 ------------------------------------------------------------------------------- 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 8060 Z= 0.255 Angle : 0.609 8.076 10948 Z= 0.346 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 : 9.97 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 (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: 0.04 (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 TRP 0.008 0.001 TRP A 234 HIS 0.008 0.001 HIS A 220 PHE 0.016 0.001 PHE R 310 TYR 0.027 0.002 TYR B 59 ARG 0.012 0.000 ARG A 20 *********************** 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 : 0.965 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: 0.8006 (m-80) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2295 time to fit residues: 42.2945 Evaluate side-chains 121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.184600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142230 restraints weight = 9220.267| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.70 r_work: 0.3294 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8060 Z= 0.198 Angle : 0.551 6.534 10948 Z= 0.290 Chirality : 0.042 0.140 1261 Planarity : 0.004 0.030 1397 Dihedral : 4.076 18.794 1130 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.49 % Allowed : 8.59 % 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 (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: 0.27 (0.27), residues: 1019 helix: 2.05 (0.26), residues: 424 sheet: -0.63 (0.34), residues: 213 loop : -1.51 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.005 0.001 HIS A 220 PHE 0.016 0.001 PHE R 310 TYR 0.028 0.001 TYR R 80 ARG 0.005 0.000 ARG A 20 *********************** 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 144 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6744 (mm) REVERT: R 191 GLU cc_start: 0.4890 (pp20) cc_final: 0.3981 (pm20) REVERT: R 234 ILE cc_start: 0.7924 (mm) cc_final: 0.7541 (pt) REVERT: A 31 GLN cc_start: 0.8150 (tp-100) cc_final: 0.7654 (tp-100) REVERT: A 381 ASP cc_start: 0.8776 (t0) cc_final: 0.8523 (t0) REVERT: A 386 MET cc_start: 0.8278 (tmm) cc_final: 0.8038 (tmm) REVERT: B 243 THR cc_start: 0.8827 (p) cc_final: 0.8620 (p) REVERT: B 264 TYR cc_start: 0.8674 (m-80) cc_final: 0.8336 (m-80) REVERT: N 73 ASP cc_start: 0.7719 (t70) cc_final: 0.7518 (t0) REVERT: N 82 GLN cc_start: 0.8330 (tp40) cc_final: 0.7920 (tp-100) outliers start: 12 outliers final: 7 residues processed: 137 average time/residue: 0.2076 time to fit residues: 38.4555 Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ** 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 = 0.4056 r_free = 0.4056 target = 0.181472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140104 restraints weight = 9264.107| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.71 r_work: 0.3263 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8060 Z= 0.286 Angle : 0.555 6.554 10948 Z= 0.293 Chirality : 0.042 0.149 1261 Planarity : 0.004 0.030 1397 Dihedral : 4.126 19.688 1130 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.99 % Allowed : 11.58 % Favored : 86.43 % 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: 0.21 (0.27), residues: 1019 helix: 1.96 (0.26), residues: 428 sheet: -0.58 (0.34), residues: 215 loop : -1.60 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.005 0.001 HIS A 220 PHE 0.018 0.002 PHE R 310 TYR 0.028 0.002 TYR B 59 ARG 0.004 0.000 ARG A 20 *********************** 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 138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.6819 (mm) REVERT: R 183 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8262 (tp) REVERT: R 191 GLU cc_start: 0.4835 (pp20) cc_final: 0.3903 (pm20) REVERT: R 234 ILE cc_start: 0.7966 (mm) cc_final: 0.7625 (pt) REVERT: A 31 GLN cc_start: 0.8232 (tp-100) cc_final: 0.7731 (tp-100) REVERT: A 381 ASP cc_start: 0.8834 (t70) cc_final: 0.8590 (t0) REVERT: A 386 MET cc_start: 0.8227 (tmm) cc_final: 0.7982 (tmm) REVERT: B 243 THR cc_start: 0.8825 (p) cc_final: 0.8609 (p) REVERT: B 262 MET cc_start: 0.8272 (ppp) cc_final: 0.8040 (ptm) REVERT: N 73 ASP cc_start: 0.7814 (t70) cc_final: 0.7599 (t0) outliers start: 16 outliers final: 11 residues processed: 130 average time/residue: 0.2212 time to fit residues: 39.0364 Evaluate side-chains 132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 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 83 MET 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 94 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 0.0570 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 ** 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 = 0.4070 r_free = 0.4070 target = 0.182865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.140499 restraints weight = 9235.869| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.84 r_work: 0.3274 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8060 Z= 0.196 Angle : 0.510 6.518 10948 Z= 0.268 Chirality : 0.041 0.160 1261 Planarity : 0.003 0.030 1397 Dihedral : 3.975 18.666 1130 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.86 % Allowed : 12.95 % Favored : 84.18 % 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: 0.39 (0.27), residues: 1019 helix: 2.20 (0.26), residues: 421 sheet: -0.48 (0.34), residues: 215 loop : -1.55 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 PHE 0.018 0.001 PHE R 310 TYR 0.025 0.001 TYR R 80 ARG 0.004 0.000 ARG A 20 *********************** 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 152 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6875 (mm) REVERT: R 191 GLU cc_start: 0.4843 (pp20) cc_final: 0.3958 (pm20) REVERT: R 234 ILE cc_start: 0.8029 (mm) cc_final: 0.7622 (pt) REVERT: R 331 TYR cc_start: 0.6299 (OUTLIER) cc_final: 0.5594 (t80) REVERT: A 31 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7728 (tp-100) REVERT: A 372 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7603 (mp) REVERT: A 381 ASP cc_start: 0.8793 (t70) cc_final: 0.8521 (t0) REVERT: B 243 THR cc_start: 0.8766 (p) cc_final: 0.8560 (p) REVERT: B 262 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7939 (ptp) REVERT: B 264 TYR cc_start: 0.8706 (m-80) cc_final: 0.8181 (m-80) REVERT: N 73 ASP cc_start: 0.7769 (t70) cc_final: 0.7569 (t0) outliers start: 23 outliers final: 10 residues processed: 145 average time/residue: 0.2019 time to fit residues: 39.6138 Evaluate side-chains 138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 R residue 289 LEU Chi-restraints excluded: chain R residue 331 TYR Chi-restraints excluded: chain A residue 372 ILE 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 83 MET 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 94 optimal weight: 0.0030 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.183827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142077 restraints weight = 9197.261| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.64 r_work: 0.3311 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8060 Z= 0.165 Angle : 0.508 6.527 10948 Z= 0.264 Chirality : 0.040 0.183 1261 Planarity : 0.003 0.029 1397 Dihedral : 3.863 17.531 1130 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.11 % Allowed : 14.20 % Favored : 82.69 % 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: 0.50 (0.27), residues: 1019 helix: 2.25 (0.26), residues: 422 sheet: -0.33 (0.33), residues: 215 loop : -1.51 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE R 310 TYR 0.026 0.001 TYR R 80 ARG 0.005 0.000 ARG A 20 *********************** 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 155 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7060 (mm) REVERT: R 191 GLU cc_start: 0.4840 (pp20) cc_final: 0.3995 (pm20) REVERT: R 234 ILE cc_start: 0.8004 (mm) cc_final: 0.7619 (pt) REVERT: R 331 TYR cc_start: 0.6232 (OUTLIER) cc_final: 0.5576 (t80) REVERT: A 31 GLN cc_start: 0.8229 (tp-100) cc_final: 0.7733 (tp-100) REVERT: A 60 MET cc_start: 0.5102 (ptt) cc_final: 0.4444 (ptt) REVERT: A 381 ASP cc_start: 0.8788 (t70) cc_final: 0.8505 (t0) REVERT: B 217 MET cc_start: 0.8245 (pmm) cc_final: 0.8037 (pmm) REVERT: B 243 THR cc_start: 0.8767 (p) cc_final: 0.8537 (p) REVERT: B 262 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7869 (ptp) REVERT: B 264 TYR cc_start: 0.8648 (m-80) cc_final: 0.8150 (m-80) outliers start: 25 outliers final: 12 residues processed: 143 average time/residue: 0.2044 time to fit residues: 39.4826 Evaluate side-chains 138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 R residue 331 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER 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 53 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.0570 chunk 49 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 96 optimal weight: 0.1980 chunk 23 optimal weight: 0.0070 chunk 10 optimal weight: 0.8980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4096 r_free = 0.4096 target = 0.185587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143502 restraints weight = 9149.131| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.67 r_work: 0.3327 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8060 Z= 0.137 Angle : 0.490 7.741 10948 Z= 0.254 Chirality : 0.040 0.143 1261 Planarity : 0.003 0.030 1397 Dihedral : 3.738 17.330 1130 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.37 % Allowed : 15.69 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.27), residues: 1019 helix: 2.32 (0.26), residues: 421 sheet: -0.22 (0.34), residues: 215 loop : -1.47 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.003 0.000 HIS A 357 PHE 0.015 0.001 PHE R 310 TYR 0.026 0.001 TYR R 80 ARG 0.007 0.000 ARG A 20 *********************** 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 149 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6752 (mm) REVERT: R 120 MET cc_start: 0.7022 (mmm) cc_final: 0.6560 (mmt) REVERT: R 191 GLU cc_start: 0.4741 (pp20) cc_final: 0.3841 (pm20) REVERT: R 234 ILE cc_start: 0.7968 (mm) cc_final: 0.7583 (pt) REVERT: R 331 TYR cc_start: 0.6178 (OUTLIER) cc_final: 0.5590 (t80) REVERT: A 31 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7709 (tp-100) REVERT: A 60 MET cc_start: 0.5196 (ptt) cc_final: 0.4979 (ptt) REVERT: B 13 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7974 (mm-40) REVERT: B 234 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.7646 (t80) REVERT: B 243 THR cc_start: 0.8778 (p) cc_final: 0.8547 (p) REVERT: B 262 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7827 (ptp) REVERT: B 264 TYR cc_start: 0.8596 (m-80) cc_final: 0.8133 (m-80) REVERT: N 31 ASN cc_start: 0.9013 (m-40) cc_final: 0.8766 (m-40) REVERT: N 120 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7270 (mm110) outliers start: 19 outliers final: 14 residues processed: 140 average time/residue: 0.2082 time to fit residues: 39.2518 Evaluate side-chains 144 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 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 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 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 0.0070 chunk 12 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1604 ------------------------------------------------------------------------------- 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 ** 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 = 0.4067 r_free = 0.4067 target = 0.182377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139637 restraints weight = 9275.669| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.69 r_work: 0.3275 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8060 Z= 0.269 Angle : 0.542 6.551 10948 Z= 0.282 Chirality : 0.042 0.145 1261 Planarity : 0.003 0.029 1397 Dihedral : 3.921 18.338 1130 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.11 % Allowed : 15.69 % Favored : 81.20 % 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: 0.52 (0.27), residues: 1019 helix: 2.20 (0.26), residues: 422 sheet: -0.14 (0.34), residues: 204 loop : -1.52 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.015 0.002 PHE R 310 TYR 0.023 0.002 TYR R 80 ARG 0.006 0.000 ARG A 20 *********************** 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 147 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7021 (mm) REVERT: R 120 MET cc_start: 0.7325 (mmm) cc_final: 0.7102 (mpp) REVERT: R 191 GLU cc_start: 0.4839 (pp20) cc_final: 0.3891 (pm20) REVERT: R 234 ILE cc_start: 0.7953 (mm) cc_final: 0.7574 (pt) REVERT: R 331 TYR cc_start: 0.6523 (OUTLIER) cc_final: 0.5856 (t80) REVERT: A 31 GLN cc_start: 0.8231 (tp-100) cc_final: 0.7960 (tp-100) REVERT: A 60 MET cc_start: 0.5390 (ptt) cc_final: 0.5180 (ptt) REVERT: B 13 GLN cc_start: 0.8335 (pp30) cc_final: 0.8032 (mm-40) REVERT: B 234 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.7799 (t80) REVERT: B 243 THR cc_start: 0.8792 (p) cc_final: 0.8546 (p) REVERT: B 262 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8027 (ptp) outliers start: 25 outliers final: 20 residues processed: 135 average time/residue: 0.2020 time to fit residues: 37.5277 Evaluate side-chains 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 R residue 342 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU 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 11 LEU 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 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 57 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.182720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.140202 restraints weight = 9230.835| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.66 r_work: 0.3285 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8060 Z= 0.212 Angle : 0.518 7.437 10948 Z= 0.269 Chirality : 0.040 0.143 1261 Planarity : 0.003 0.029 1397 Dihedral : 3.875 18.077 1130 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.62 % Allowed : 16.94 % Favored : 80.45 % 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: 0.58 (0.27), residues: 1019 helix: 2.27 (0.26), residues: 422 sheet: -0.18 (0.34), residues: 210 loop : -1.48 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE R 310 TYR 0.026 0.001 TYR R 80 ARG 0.008 0.000 ARG A 20 *********************** 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 146 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: R 88 LEU cc_start: 0.7482 (mm) cc_final: 0.7140 (mm) REVERT: R 92 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6842 (mm) REVERT: R 191 GLU cc_start: 0.4723 (pp20) cc_final: 0.3811 (pm20) REVERT: R 234 ILE cc_start: 0.7946 (mm) cc_final: 0.7564 (pt) REVERT: R 331 TYR cc_start: 0.6524 (OUTLIER) cc_final: 0.5827 (t80) REVERT: A 31 GLN cc_start: 0.8392 (tp-100) cc_final: 0.7943 (tp-100) REVERT: B 234 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.7961 (t80) REVERT: B 243 THR cc_start: 0.8808 (p) cc_final: 0.8556 (p) REVERT: B 262 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8040 (ptp) outliers start: 21 outliers final: 15 residues processed: 136 average time/residue: 0.2062 time to fit residues: 38.0416 Evaluate side-chains 140 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 55 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.181345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.138655 restraints weight = 9323.001| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.68 r_work: 0.3262 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8060 Z= 0.297 Angle : 0.568 7.579 10948 Z= 0.295 Chirality : 0.042 0.146 1261 Planarity : 0.004 0.031 1397 Dihedral : 4.024 19.234 1130 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.74 % Allowed : 17.68 % Favored : 79.58 % 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: 0.45 (0.27), residues: 1019 helix: 2.18 (0.26), residues: 421 sheet: -0.24 (0.34), residues: 210 loop : -1.56 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.004 0.001 HIS B 62 PHE 0.015 0.002 PHE R 310 TYR 0.026 0.002 TYR R 80 ARG 0.007 0.000 ARG A 20 *********************** 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 144 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6855 (mm) REVERT: R 183 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8294 (tp) REVERT: R 191 GLU cc_start: 0.5009 (pp20) cc_final: 0.4058 (pm20) REVERT: R 234 ILE cc_start: 0.7972 (mm) cc_final: 0.7609 (pt) REVERT: R 331 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.6081 (t80) REVERT: A 31 GLN cc_start: 0.8425 (tp-100) cc_final: 0.7987 (tp-100) REVERT: A 381 ASP cc_start: 0.8792 (t70) cc_final: 0.8541 (t0) REVERT: B 234 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8065 (t80) REVERT: B 243 THR cc_start: 0.8841 (p) cc_final: 0.8581 (p) REVERT: B 262 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8061 (ptm) outliers start: 22 outliers final: 15 residues processed: 134 average time/residue: 0.1904 time to fit residues: 35.6705 Evaluate side-chains 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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 55 LEU 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 16 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 0.0370 chunk 99 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 ** 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 = 0.4074 r_free = 0.4074 target = 0.183227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140034 restraints weight = 9150.924| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.64 r_work: 0.3291 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8060 Z= 0.183 Angle : 0.528 8.135 10948 Z= 0.274 Chirality : 0.040 0.142 1261 Planarity : 0.003 0.034 1397 Dihedral : 3.892 17.549 1130 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.49 % Allowed : 18.18 % Favored : 79.33 % 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: 0.57 (0.27), residues: 1019 helix: 2.31 (0.26), residues: 421 sheet: -0.17 (0.34), residues: 211 loop : -1.53 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.020 0.001 PHE R 195 TYR 0.025 0.001 TYR R 80 ARG 0.008 0.000 ARG A 20 ********************** 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 145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: R 92 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6697 (mm) REVERT: R 191 GLU cc_start: 0.4922 (pp20) cc_final: 0.3954 (pm20) REVERT: R 195 PHE cc_start: 0.8345 (t80) cc_final: 0.8126 (t80) REVERT: R 234 ILE cc_start: 0.7951 (mm) cc_final: 0.7591 (pt) REVERT: R 280 ARG cc_start: 0.7182 (mmp80) cc_final: 0.6978 (mmp-170) REVERT: R 331 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.6023 (t80) REVERT: A 31 GLN cc_start: 0.8395 (tp-100) cc_final: 0.7950 (tp-100) REVERT: A 381 ASP cc_start: 0.8792 (t70) cc_final: 0.8458 (t0) REVERT: B 234 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8024 (t80) REVERT: B 243 THR cc_start: 0.8788 (p) cc_final: 0.8537 (p) REVERT: B 262 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7918 (ptp) REVERT: B 264 TYR cc_start: 0.8671 (m-80) cc_final: 0.8216 (m-80) outliers start: 20 outliers final: 15 residues processed: 136 average time/residue: 0.2023 time to fit residues: 37.7117 Evaluate side-chains 142 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 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 55 LEU 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 56 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4070 r_free = 0.4070 target = 0.182862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.139527 restraints weight = 9181.462| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.66 r_work: 0.3298 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8060 Z= 0.200 Angle : 0.531 7.839 10948 Z= 0.275 Chirality : 0.041 0.143 1261 Planarity : 0.003 0.035 1397 Dihedral : 3.868 17.357 1130 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.62 % Allowed : 18.56 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.61 (0.27), residues: 1019 helix: 2.31 (0.26), residues: 421 sheet: -0.08 (0.34), residues: 205 loop : -1.51 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.018 0.001 PHE R 195 TYR 0.025 0.001 TYR R 80 ARG 0.008 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3940.91 seconds wall clock time: 70 minutes 40.73 seconds (4240.73 seconds total)