Starting phenix.real_space_refine on Wed Feb 12 03:12:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eib_31145/02_2025/7eib_31145.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eib_31145/02_2025/7eib_31145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eib_31145/02_2025/7eib_31145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eib_31145/02_2025/7eib_31145.map" model { file = "/net/cci-nas-00/data/ceres_data/7eib_31145/02_2025/7eib_31145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eib_31145/02_2025/7eib_31145.cif" } resolution = 3.0 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= 0.002 sd= 0.028 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 37 5.16 5 C 4628 2.51 5 N 1253 2.21 5 O 1286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7204 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2419 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 5} Chain: "B" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1880 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2478 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 91 Chain: "E" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 4.51, per 1000 atoms: 0.63 Number of scatterers: 7204 At special positions: 0 Unit cell: (91.8, 82.08, 125.28, 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 37 16.00 O 1286 8.00 N 1253 7.00 C 4628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 189 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 1.0 seconds 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1762 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 48.9% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 30 through 64 removed outlier: 3.592A pdb=" N ASP A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 70 through 89 removed outlier: 3.505A pdb=" N TYR A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.829A pdb=" N TRP A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 141 removed outlier: 3.795A pdb=" N ASN A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 149 through 168 removed outlier: 3.670A pdb=" N GLN A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.672A pdb=" N PHE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 239 removed outlier: 4.013A pdb=" N THR A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 278 removed outlier: 3.757A pdb=" N VAL A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 283 through 302 removed outlier: 3.717A pdb=" N GLN A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.982A pdb=" N SER A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'B' and resid 6 through 33 removed outlier: 3.842A pdb=" N GLN B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.596A pdb=" N ASN B 216 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP B 217 " --> pdb=" O CYS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 246 removed outlier: 3.903A pdb=" N GLN B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 250 removed outlier: 3.661A pdb=" N ARG B 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 250' Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.893A pdb=" N SER B 319 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 358 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'E' and resid 12 through 24 removed outlier: 3.562A pdb=" N GLU E 17 " --> pdb=" O ARG E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 180 Processing sheet with id=AA2, first strand: chain 'B' and resid 184 through 191 removed outlier: 6.197A pdb=" N LEU B 34 " --> pdb=" O HIS B 197 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE B 199 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N VAL B 201 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU B 38 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE B 222 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 39 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ASP B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE B 221 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE B 257 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 223 " --> pdb=" O PHE B 257 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN B 259 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL B 225 " --> pdb=" O ASN B 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51 Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.571A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.902A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.749A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.739A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.917A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.849A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1170 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: 2.28 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1165 1.31 - 1.44: 2056 1.44 - 1.57: 4097 1.57 - 1.69: 0 1.69 - 1.82: 48 Bond restraints: 7366 Sorted by residual: bond pdb=" CA PRO D 4 " pdb=" C PRO D 4 " ideal model delta sigma weight residual 1.520 1.458 0.062 1.24e-02 6.50e+03 2.48e+01 bond pdb=" N CYS B 332 " pdb=" CA CYS B 332 " ideal model delta sigma weight residual 1.454 1.402 0.052 1.23e-02 6.61e+03 1.78e+01 bond pdb=" C PRO D 8 " pdb=" O PRO D 8 " ideal model delta sigma weight residual 1.238 1.186 0.052 1.36e-02 5.41e+03 1.44e+01 bond pdb=" C PHE D 6 " pdb=" O PHE D 6 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.28e-02 6.10e+03 1.42e+01 bond pdb=" CA SER D 7 " pdb=" CB SER D 7 " ideal model delta sigma weight residual 1.533 1.477 0.056 1.49e-02 4.50e+03 1.40e+01 ... (remaining 7361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 9849 2.64 - 5.29: 154 5.29 - 7.93: 15 7.93 - 10.58: 1 10.58 - 13.22: 2 Bond angle restraints: 10021 Sorted by residual: angle pdb=" C PRO D 3 " pdb=" N PRO D 4 " pdb=" CA PRO D 4 " ideal model delta sigma weight residual 120.14 109.58 10.56 1.06e+00 8.90e-01 9.92e+01 angle pdb=" CA PRO B 295 " pdb=" N PRO B 295 " pdb=" CD PRO B 295 " ideal model delta sigma weight residual 112.00 100.07 11.93 1.40e+00 5.10e-01 7.26e+01 angle pdb=" N VAL B 334 " pdb=" CA VAL B 334 " pdb=" C VAL B 334 " ideal model delta sigma weight residual 110.62 115.36 -4.74 1.02e+00 9.61e-01 2.16e+01 angle pdb=" CA PRO D 8 " pdb=" C PRO D 8 " pdb=" O PRO D 8 " ideal model delta sigma weight residual 120.03 113.31 6.72 1.45e+00 4.76e-01 2.14e+01 angle pdb=" C VAL B 334 " pdb=" CA VAL B 334 " pdb=" CB VAL B 334 " ideal model delta sigma weight residual 112.14 106.19 5.95 1.35e+00 5.49e-01 1.94e+01 ... (remaining 10016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 3991 16.96 - 33.92: 287 33.92 - 50.88: 34 50.88 - 67.84: 15 67.84 - 84.80: 7 Dihedral angle restraints: 4334 sinusoidal: 1628 harmonic: 2706 Sorted by residual: dihedral pdb=" CA ILE A 97 " pdb=" C ILE A 97 " pdb=" N TRP A 98 " pdb=" CA TRP A 98 " ideal model delta harmonic sigma weight residual 180.00 150.12 29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA LEU A 326 " pdb=" C LEU A 326 " pdb=" N TYR A 327 " pdb=" CA TYR A 327 " ideal model delta harmonic sigma weight residual 180.00 150.71 29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ASN C 295 " pdb=" C ASN C 295 " pdb=" N VAL C 296 " pdb=" CA VAL C 296 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 4331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 930 0.063 - 0.125: 196 0.125 - 0.188: 23 0.188 - 0.251: 2 0.251 - 0.313: 1 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CA PRO D 8 " pdb=" N PRO D 8 " pdb=" C PRO D 8 " pdb=" CB PRO D 8 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA PHE D 9 " pdb=" N PHE D 9 " pdb=" C PHE D 9 " pdb=" CB PHE D 9 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB VAL A 128 " pdb=" CA VAL A 128 " pdb=" CG1 VAL A 128 " pdb=" CG2 VAL A 128 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 1149 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 326 " 0.059 2.00e-02 2.50e+03 1.17e-01 1.36e+02 pdb=" C LEU A 326 " -0.202 2.00e-02 2.50e+03 pdb=" O LEU A 326 " 0.077 2.00e-02 2.50e+03 pdb=" N TYR A 327 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 206 " 0.024 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C LEU A 206 " -0.081 2.00e-02 2.50e+03 pdb=" O LEU A 206 " 0.030 2.00e-02 2.50e+03 pdb=" N ASN A 207 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 208 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.92e+01 pdb=" C ILE A 208 " 0.076 2.00e-02 2.50e+03 pdb=" O ILE A 208 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU A 209 " -0.026 2.00e-02 2.50e+03 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2122 2.82 - 3.34: 7243 3.34 - 3.86: 12557 3.86 - 4.38: 14516 4.38 - 4.90: 24893 Nonbonded interactions: 61331 Sorted by model distance: nonbonded pdb=" OD2 ASP A 134 " pdb=" OH TYR B 358 " model vdw 2.306 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.306 3.040 nonbonded pdb=" NH2 ARG B 208 " pdb=" OD1 ASP B 239 " model vdw 2.309 3.120 nonbonded pdb=" NH1 ARG C 251 " pdb=" OE1 GLU C 260 " model vdw 2.316 3.120 nonbonded pdb=" NH1 ARG A 176 " pdb=" O GLY D 5 " model vdw 2.333 3.120 ... (remaining 61326 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: 0.400 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.700 Find NCS groups from input model: 0.070 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:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 : 0.005 0.071 7366 Z= 0.348 Angle : 0.855 13.224 10021 Z= 0.530 Chirality : 0.051 0.313 1152 Planarity : 0.010 0.117 1276 Dihedral : 12.654 84.801 2569 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.27 % Allowed : 1.48 % Favored : 98.25 % 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: -0.34 (0.26), residues: 914 helix: -0.34 (0.22), residues: 412 sheet: 0.23 (0.35), residues: 195 loop : -0.05 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 211 HIS 0.005 0.001 HIS C 142 PHE 0.026 0.003 PHE C 235 TYR 0.026 0.006 TYR C 289 ARG 0.055 0.008 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.827 Fit side-chains REVERT: A 47 ILE cc_start: 0.8050 (mt) cc_final: 0.7846 (mp) REVERT: A 84 LEU cc_start: 0.8250 (tp) cc_final: 0.8028 (tt) REVERT: A 102 ASN cc_start: 0.7763 (t0) cc_final: 0.7396 (t0) REVERT: A 111 ARG cc_start: 0.7887 (mtt-85) cc_final: 0.7584 (mtt180) REVERT: A 298 ASN cc_start: 0.7450 (t0) cc_final: 0.7175 (t0) REVERT: D 9 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6943 (m-80) REVERT: B 188 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7786 (mttm) REVERT: B 195 ASN cc_start: 0.7521 (m-40) cc_final: 0.7255 (m110) REVERT: B 252 ILE cc_start: 0.8191 (mt) cc_final: 0.7904 (mm) REVERT: B 253 SER cc_start: 0.8193 (m) cc_final: 0.7800 (t) REVERT: B 300 ARG cc_start: 0.8164 (mtm180) cc_final: 0.7936 (mtm180) REVERT: B 348 ASP cc_start: 0.7714 (t70) cc_final: 0.7180 (t0) REVERT: C 111 TYR cc_start: 0.8262 (m-80) cc_final: 0.7889 (m-80) REVERT: C 153 ASP cc_start: 0.6985 (t70) cc_final: 0.6744 (t70) REVERT: C 186 ASP cc_start: 0.7128 (m-30) cc_final: 0.6879 (m-30) REVERT: C 204 CYS cc_start: 0.7830 (m) cc_final: 0.7624 (m) REVERT: C 212 ASP cc_start: 0.6803 (t0) cc_final: 0.6410 (t70) REVERT: C 239 ASN cc_start: 0.7246 (m-40) cc_final: 0.6715 (m-40) REVERT: C 295 ASN cc_start: 0.6557 (p0) cc_final: 0.6351 (p0) REVERT: C 303 ASP cc_start: 0.6614 (t0) cc_final: 0.6285 (m-30) outliers start: 2 outliers final: 1 residues processed: 207 average time/residue: 1.1284 time to fit residues: 246.9342 Evaluate side-chains 173 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain D residue 9 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 308 ASN B 246 ASN B 259 ASN B 359 ASN C 110 ASN C 119 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.137329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117831 restraints weight = 9585.390| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.05 r_work: 0.3363 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7366 Z= 0.288 Angle : 0.657 7.019 10021 Z= 0.354 Chirality : 0.046 0.187 1152 Planarity : 0.005 0.044 1276 Dihedral : 6.128 52.021 1006 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.88 % Allowed : 12.10 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 914 helix: 1.31 (0.25), residues: 412 sheet: 0.24 (0.35), residues: 193 loop : 0.37 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 169 HIS 0.006 0.001 HIS C 91 PHE 0.014 0.002 PHE A 173 TYR 0.022 0.002 TYR A 75 ARG 0.008 0.001 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 111 ARG cc_start: 0.8088 (mtt-85) cc_final: 0.7799 (mtt180) REVERT: A 176 ARG cc_start: 0.8477 (tpp-160) cc_final: 0.8073 (ttt180) REVERT: A 179 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7989 (mt0) REVERT: A 232 ARG cc_start: 0.7372 (ttt-90) cc_final: 0.7031 (ttt180) REVERT: A 298 ASN cc_start: 0.7841 (t0) cc_final: 0.7635 (t160) REVERT: B 188 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8416 (mttm) REVERT: B 252 ILE cc_start: 0.8340 (mt) cc_final: 0.8101 (mm) REVERT: C 105 TYR cc_start: 0.8806 (t80) cc_final: 0.8557 (t80) REVERT: C 111 TYR cc_start: 0.8657 (m-80) cc_final: 0.8261 (m-80) REVERT: C 153 ASP cc_start: 0.7527 (t70) cc_final: 0.7195 (t0) REVERT: C 154 ASP cc_start: 0.7837 (m-30) cc_final: 0.7593 (m-30) REVERT: C 189 SER cc_start: 0.8527 (t) cc_final: 0.8326 (p) REVERT: C 212 ASP cc_start: 0.7593 (t0) cc_final: 0.7137 (t70) REVERT: C 303 ASP cc_start: 0.7380 (t0) cc_final: 0.6903 (m-30) REVERT: C 335 PHE cc_start: 0.7723 (m-10) cc_final: 0.7492 (m-80) outliers start: 14 outliers final: 9 residues processed: 176 average time/residue: 1.0910 time to fit residues: 203.4264 Evaluate side-chains 169 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain C residue 161 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 68 optimal weight: 0.0570 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN B 246 ASN B 259 ASN B 359 ASN C 91 HIS C 230 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118283 restraints weight = 9726.654| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.08 r_work: 0.3376 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7366 Z= 0.211 Angle : 0.566 5.654 10021 Z= 0.307 Chirality : 0.043 0.174 1152 Planarity : 0.004 0.041 1276 Dihedral : 5.458 39.926 1004 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.28 % Allowed : 14.92 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.28), residues: 914 helix: 1.75 (0.26), residues: 407 sheet: 0.11 (0.36), residues: 186 loop : 0.33 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 169 HIS 0.004 0.001 HIS C 91 PHE 0.013 0.001 PHE A 173 TYR 0.019 0.002 TYR A 266 ARG 0.006 0.001 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8187 (mt) cc_final: 0.7895 (mm) REVERT: A 150 ARG cc_start: 0.7976 (mtp-110) cc_final: 0.7730 (mtm110) REVERT: A 179 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7929 (mt0) REVERT: A 232 ARG cc_start: 0.7352 (ttt-90) cc_final: 0.6972 (ttt180) REVERT: B 188 LYS cc_start: 0.8700 (mtmm) cc_final: 0.8448 (mttm) REVERT: B 252 ILE cc_start: 0.8162 (mt) cc_final: 0.7945 (mm) REVERT: B 297 GLU cc_start: 0.8193 (pt0) cc_final: 0.7763 (pm20) REVERT: C 105 TYR cc_start: 0.8788 (t80) cc_final: 0.8504 (t80) REVERT: C 111 TYR cc_start: 0.8612 (m-80) cc_final: 0.8181 (m-80) REVERT: C 153 ASP cc_start: 0.7490 (t70) cc_final: 0.7172 (t0) REVERT: C 154 ASP cc_start: 0.7876 (m-30) cc_final: 0.7585 (m-30) REVERT: C 188 MET cc_start: 0.8155 (mmm) cc_final: 0.7899 (mmp) REVERT: C 191 SER cc_start: 0.8455 (p) cc_final: 0.8207 (t) REVERT: C 212 ASP cc_start: 0.7620 (t0) cc_final: 0.7171 (t70) REVERT: C 254 ASP cc_start: 0.7378 (t0) cc_final: 0.7140 (t0) REVERT: C 303 ASP cc_start: 0.7413 (t0) cc_final: 0.6956 (m-30) outliers start: 17 outliers final: 11 residues processed: 169 average time/residue: 1.1759 time to fit residues: 210.3004 Evaluate side-chains 161 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 294 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 0.0370 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 216 ASN B 246 ASN B 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119619 restraints weight = 9713.708| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.11 r_work: 0.3373 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7366 Z= 0.211 Angle : 0.547 6.269 10021 Z= 0.293 Chirality : 0.042 0.220 1152 Planarity : 0.005 0.060 1276 Dihedral : 5.012 26.609 1004 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.17 % Allowed : 15.32 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.29), residues: 914 helix: 2.00 (0.26), residues: 406 sheet: 0.09 (0.37), residues: 174 loop : 0.28 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 82 HIS 0.003 0.001 HIS A 199 PHE 0.026 0.002 PHE A 43 TYR 0.019 0.001 TYR A 75 ARG 0.006 0.001 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8148 (mt) cc_final: 0.7884 (mm) REVERT: A 111 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7812 (mtp85) REVERT: A 138 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7905 (t) REVERT: A 150 ARG cc_start: 0.7939 (mtp-110) cc_final: 0.7678 (mtm180) REVERT: A 176 ARG cc_start: 0.8456 (tpp-160) cc_final: 0.8145 (ttt90) REVERT: A 232 ARG cc_start: 0.7360 (ttt-90) cc_final: 0.6911 (ttt180) REVERT: B 29 VAL cc_start: 0.8052 (t) cc_final: 0.7846 (p) REVERT: B 188 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8330 (mttm) REVERT: B 233 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7327 (tp) REVERT: B 297 GLU cc_start: 0.8202 (pt0) cc_final: 0.7768 (pm20) REVERT: C 105 TYR cc_start: 0.8767 (t80) cc_final: 0.8536 (t80) REVERT: C 111 TYR cc_start: 0.8629 (m-80) cc_final: 0.8209 (m-80) REVERT: C 137 ARG cc_start: 0.7795 (ttm110) cc_final: 0.7572 (tpp-160) REVERT: C 153 ASP cc_start: 0.7619 (t70) cc_final: 0.7304 (t70) REVERT: C 160 SER cc_start: 0.8497 (p) cc_final: 0.8186 (t) REVERT: C 188 MET cc_start: 0.7991 (mmm) cc_final: 0.7771 (mmp) REVERT: C 254 ASP cc_start: 0.7416 (t0) cc_final: 0.7182 (t0) REVERT: C 303 ASP cc_start: 0.7536 (t0) cc_final: 0.7094 (m-30) REVERT: C 327 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8461 (t) outliers start: 31 outliers final: 14 residues processed: 180 average time/residue: 1.0527 time to fit residues: 201.0570 Evaluate side-chains 171 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 298 ASN A 308 ASN A 329 GLN B 246 ASN B 259 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.136472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117095 restraints weight = 9726.490| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.15 r_work: 0.3334 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7366 Z= 0.268 Angle : 0.561 7.412 10021 Z= 0.302 Chirality : 0.043 0.158 1152 Planarity : 0.005 0.052 1276 Dihedral : 4.889 27.633 1000 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.63 % Allowed : 18.01 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.28), residues: 914 helix: 2.00 (0.26), residues: 406 sheet: -0.05 (0.38), residues: 167 loop : 0.09 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 169 HIS 0.004 0.001 HIS A 267 PHE 0.027 0.002 PHE A 43 TYR 0.021 0.002 TYR A 75 ARG 0.007 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.749 Fit side-chains REVERT: A 56 LEU cc_start: 0.8102 (mt) cc_final: 0.7851 (mm) REVERT: A 111 ARG cc_start: 0.8064 (mtt-85) cc_final: 0.7738 (mtt180) REVERT: A 138 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7899 (t) REVERT: A 150 ARG cc_start: 0.7935 (mtp-110) cc_final: 0.7666 (mtm180) REVERT: A 192 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8336 (tp) REVERT: A 232 ARG cc_start: 0.7399 (ttt-90) cc_final: 0.6923 (ttt180) REVERT: B 188 LYS cc_start: 0.8609 (mtmm) cc_final: 0.8360 (mttm) REVERT: B 297 GLU cc_start: 0.8131 (pt0) cc_final: 0.7683 (pm20) REVERT: C 105 TYR cc_start: 0.8779 (t80) cc_final: 0.8477 (t80) REVERT: C 111 TYR cc_start: 0.8608 (m-80) cc_final: 0.8217 (m-80) REVERT: C 137 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7613 (tpp-160) REVERT: C 153 ASP cc_start: 0.7704 (t70) cc_final: 0.7405 (t70) REVERT: C 154 ASP cc_start: 0.7752 (m-30) cc_final: 0.7543 (m-30) REVERT: C 160 SER cc_start: 0.8491 (p) cc_final: 0.8230 (t) REVERT: C 188 MET cc_start: 0.8077 (mmm) cc_final: 0.7841 (mmp) REVERT: C 212 ASP cc_start: 0.7599 (t0) cc_final: 0.7212 (t70) REVERT: C 254 ASP cc_start: 0.7440 (t0) cc_final: 0.7212 (t0) REVERT: C 327 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8449 (t) outliers start: 27 outliers final: 19 residues processed: 173 average time/residue: 1.1879 time to fit residues: 217.1652 Evaluate side-chains 170 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 38 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 31 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN B 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.138462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119214 restraints weight = 9649.571| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.11 r_work: 0.3385 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7366 Z= 0.243 Angle : 0.551 6.609 10021 Z= 0.296 Chirality : 0.042 0.169 1152 Planarity : 0.005 0.051 1276 Dihedral : 4.804 27.113 1000 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.03 % Allowed : 18.82 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.28), residues: 914 helix: 2.05 (0.26), residues: 406 sheet: -0.25 (0.38), residues: 167 loop : 0.06 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 169 HIS 0.003 0.001 HIS A 267 PHE 0.028 0.002 PHE A 43 TYR 0.020 0.001 TYR A 75 ARG 0.007 0.001 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.755 Fit side-chains REVERT: A 56 LEU cc_start: 0.8151 (mt) cc_final: 0.7911 (mm) REVERT: A 111 ARG cc_start: 0.8035 (mtt-85) cc_final: 0.7605 (mtt90) REVERT: A 150 ARG cc_start: 0.7931 (mtp-110) cc_final: 0.7604 (mtm180) REVERT: A 192 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8346 (tp) REVERT: A 232 ARG cc_start: 0.7460 (ttt-90) cc_final: 0.6943 (ttt180) REVERT: B 188 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8375 (mttm) REVERT: B 233 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7352 (tp) REVERT: B 297 GLU cc_start: 0.8119 (pt0) cc_final: 0.7652 (pm20) REVERT: B 356 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7951 (mtm180) REVERT: B 358 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8378 (m-80) REVERT: C 105 TYR cc_start: 0.8753 (t80) cc_final: 0.8461 (t80) REVERT: C 111 TYR cc_start: 0.8640 (m-80) cc_final: 0.8246 (m-80) REVERT: C 137 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7620 (tpp-160) REVERT: C 150 ARG cc_start: 0.8669 (mtt-85) cc_final: 0.8436 (mtp85) REVERT: C 153 ASP cc_start: 0.7708 (t70) cc_final: 0.7395 (t70) REVERT: C 154 ASP cc_start: 0.7718 (m-30) cc_final: 0.7495 (m-30) REVERT: C 160 SER cc_start: 0.8453 (p) cc_final: 0.8218 (t) REVERT: C 186 ASP cc_start: 0.7717 (m-30) cc_final: 0.7197 (m-30) REVERT: C 188 MET cc_start: 0.8109 (mmm) cc_final: 0.7843 (mmp) REVERT: C 254 ASP cc_start: 0.7467 (t0) cc_final: 0.7241 (t0) REVERT: C 327 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8423 (t) outliers start: 30 outliers final: 19 residues processed: 176 average time/residue: 1.1580 time to fit residues: 215.3567 Evaluate side-chains 178 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 358 TYR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 38 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 25 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN B 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.137056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117716 restraints weight = 9554.184| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.11 r_work: 0.3362 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7366 Z= 0.289 Angle : 0.573 6.678 10021 Z= 0.307 Chirality : 0.043 0.164 1152 Planarity : 0.005 0.053 1276 Dihedral : 4.875 29.516 1000 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.49 % Allowed : 20.30 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.28), residues: 914 helix: 1.97 (0.26), residues: 406 sheet: -0.43 (0.37), residues: 168 loop : -0.01 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 169 HIS 0.003 0.001 HIS A 267 PHE 0.021 0.002 PHE A 43 TYR 0.023 0.002 TYR A 75 ARG 0.007 0.001 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.852 Fit side-chains REVERT: A 111 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7722 (mtt180) REVERT: A 150 ARG cc_start: 0.7940 (mtp180) cc_final: 0.7633 (mtm180) REVERT: A 192 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8350 (tp) REVERT: A 232 ARG cc_start: 0.7515 (ttt-90) cc_final: 0.6944 (ttt180) REVERT: B 188 LYS cc_start: 0.8663 (mtmm) cc_final: 0.8431 (mttm) REVERT: B 297 GLU cc_start: 0.8063 (pt0) cc_final: 0.7541 (pm20) REVERT: B 348 ASP cc_start: 0.8192 (t70) cc_final: 0.7806 (t70) REVERT: C 49 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7136 (mtm-85) REVERT: C 111 TYR cc_start: 0.8626 (m-80) cc_final: 0.8229 (m-80) REVERT: C 137 ARG cc_start: 0.7835 (ttm110) cc_final: 0.7614 (tpp-160) REVERT: C 153 ASP cc_start: 0.7626 (t70) cc_final: 0.7313 (t70) REVERT: C 154 ASP cc_start: 0.7731 (m-30) cc_final: 0.7499 (m-30) REVERT: C 186 ASP cc_start: 0.7949 (m-30) cc_final: 0.7600 (m-30) REVERT: C 188 MET cc_start: 0.8156 (mmm) cc_final: 0.7879 (mmp) REVERT: C 254 ASP cc_start: 0.7562 (t0) cc_final: 0.7316 (t0) REVERT: C 327 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8490 (t) outliers start: 26 outliers final: 18 residues processed: 176 average time/residue: 1.2482 time to fit residues: 231.2243 Evaluate side-chains 178 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 38 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 48 optimal weight: 0.0470 chunk 49 optimal weight: 0.1980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN B 259 ASN C 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.139123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119802 restraints weight = 9700.307| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.12 r_work: 0.3381 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7366 Z= 0.207 Angle : 0.549 6.237 10021 Z= 0.294 Chirality : 0.042 0.162 1152 Planarity : 0.005 0.054 1276 Dihedral : 4.731 28.998 1000 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.23 % Allowed : 20.03 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.29), residues: 914 helix: 2.06 (0.26), residues: 407 sheet: -0.57 (0.37), residues: 170 loop : 0.03 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 126 HIS 0.003 0.001 HIS A 267 PHE 0.015 0.001 PHE B 189 TYR 0.017 0.001 TYR A 75 ARG 0.008 0.001 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.744 Fit side-chains REVERT: A 111 ARG cc_start: 0.7991 (mtt-85) cc_final: 0.7704 (mtt-85) REVERT: A 192 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8338 (tp) REVERT: A 232 ARG cc_start: 0.7511 (ttt-90) cc_final: 0.7110 (ttt180) REVERT: A 320 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7094 (mtm180) REVERT: B 188 LYS cc_start: 0.8643 (mtmm) cc_final: 0.8428 (mttm) REVERT: B 233 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7341 (tp) REVERT: B 348 ASP cc_start: 0.8174 (t70) cc_final: 0.7948 (t70) REVERT: C 48 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7513 (mmt90) REVERT: C 49 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7218 (mtm-85) REVERT: C 105 TYR cc_start: 0.8808 (t80) cc_final: 0.8512 (t80) REVERT: C 111 TYR cc_start: 0.8591 (m-80) cc_final: 0.8247 (m-80) REVERT: C 137 ARG cc_start: 0.7790 (ttm110) cc_final: 0.7581 (tpp-160) REVERT: C 153 ASP cc_start: 0.7601 (t70) cc_final: 0.7278 (t70) REVERT: C 154 ASP cc_start: 0.7701 (m-30) cc_final: 0.7458 (m-30) REVERT: C 186 ASP cc_start: 0.7813 (m-30) cc_final: 0.7526 (m-30) REVERT: C 188 MET cc_start: 0.8116 (mmm) cc_final: 0.7848 (mmp) REVERT: C 254 ASP cc_start: 0.7564 (t0) cc_final: 0.7312 (t0) REVERT: C 325 MET cc_start: 0.8259 (tpp) cc_final: 0.7837 (mmm) outliers start: 24 outliers final: 12 residues processed: 171 average time/residue: 1.2129 time to fit residues: 218.4421 Evaluate side-chains 176 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain D residue 6 PHE Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 0.0060 chunk 68 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN B 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.139850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.120669 restraints weight = 9717.488| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.13 r_work: 0.3349 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7366 Z= 0.210 Angle : 0.564 6.835 10021 Z= 0.301 Chirality : 0.042 0.158 1152 Planarity : 0.005 0.056 1276 Dihedral : 4.661 29.574 1000 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.82 % Allowed : 19.76 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.29), residues: 914 helix: 2.11 (0.25), residues: 407 sheet: -0.53 (0.38), residues: 168 loop : 0.04 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 126 HIS 0.003 0.001 HIS A 267 PHE 0.034 0.001 PHE A 43 TYR 0.018 0.001 TYR A 75 ARG 0.010 0.001 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.794 Fit side-chains REVERT: A 151 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7662 (ttt180) REVERT: A 176 ARG cc_start: 0.8507 (tpp-160) cc_final: 0.8256 (ttm-80) REVERT: A 192 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8360 (tp) REVERT: A 232 ARG cc_start: 0.7426 (ttt-90) cc_final: 0.7034 (ttt180) REVERT: A 320 ARG cc_start: 0.7630 (mtm-85) cc_final: 0.7050 (mtm180) REVERT: B 188 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8378 (mttm) REVERT: B 281 GLU cc_start: 0.7224 (tp30) cc_final: 0.6989 (tp30) REVERT: B 297 GLU cc_start: 0.8002 (pt0) cc_final: 0.7494 (pm20) REVERT: B 300 ARG cc_start: 0.8172 (mtp180) cc_final: 0.7954 (mtm180) REVERT: B 348 ASP cc_start: 0.8137 (t70) cc_final: 0.7865 (t70) REVERT: C 48 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7508 (mmt90) REVERT: C 49 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7165 (mtm-85) REVERT: C 105 TYR cc_start: 0.8805 (t80) cc_final: 0.8495 (t80) REVERT: C 111 TYR cc_start: 0.8577 (m-80) cc_final: 0.8228 (m-80) REVERT: C 137 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7543 (tpp-160) REVERT: C 153 ASP cc_start: 0.7598 (t70) cc_final: 0.7241 (t70) REVERT: C 154 ASP cc_start: 0.7670 (m-30) cc_final: 0.7419 (m-30) REVERT: C 163 ASP cc_start: 0.7552 (p0) cc_final: 0.7348 (p0) REVERT: C 186 ASP cc_start: 0.7765 (m-30) cc_final: 0.7393 (m-30) REVERT: C 188 MET cc_start: 0.8142 (mmm) cc_final: 0.7840 (mmp) REVERT: C 254 ASP cc_start: 0.7490 (t0) cc_final: 0.7276 (t0) outliers start: 21 outliers final: 12 residues processed: 170 average time/residue: 1.2282 time to fit residues: 220.4200 Evaluate side-chains 165 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain D residue 6 PHE Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 68 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN B 259 ASN B 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.139887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120394 restraints weight = 9825.592| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.15 r_work: 0.3345 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7366 Z= 0.271 Angle : 0.585 6.730 10021 Z= 0.311 Chirality : 0.044 0.250 1152 Planarity : 0.005 0.051 1276 Dihedral : 4.728 29.597 1000 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.69 % Allowed : 20.43 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.29), residues: 914 helix: 2.07 (0.26), residues: 407 sheet: -0.69 (0.38), residues: 170 loop : 0.01 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 126 HIS 0.003 0.001 HIS C 266 PHE 0.038 0.002 PHE A 43 TYR 0.022 0.002 TYR A 75 ARG 0.007 0.001 ARG B 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.816 Fit side-chains REVERT: A 176 ARG cc_start: 0.8511 (tpp-160) cc_final: 0.8126 (ttm-80) REVERT: A 192 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8404 (tp) REVERT: A 232 ARG cc_start: 0.7510 (ttt-90) cc_final: 0.7107 (ttt180) REVERT: A 320 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7092 (mtm180) REVERT: B 188 LYS cc_start: 0.8657 (mtmm) cc_final: 0.8422 (mttm) REVERT: B 281 GLU cc_start: 0.7241 (tp30) cc_final: 0.6995 (tp30) REVERT: B 297 GLU cc_start: 0.7979 (pt0) cc_final: 0.7546 (pm20) REVERT: B 348 ASP cc_start: 0.8175 (t70) cc_final: 0.7950 (t70) REVERT: C 48 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7561 (mmt90) REVERT: C 49 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7210 (mtm-85) REVERT: C 105 TYR cc_start: 0.8821 (t80) cc_final: 0.8521 (t80) REVERT: C 111 TYR cc_start: 0.8604 (m-80) cc_final: 0.8213 (m-80) REVERT: C 137 ARG cc_start: 0.7820 (ttm110) cc_final: 0.7600 (tpp-160) REVERT: C 153 ASP cc_start: 0.7718 (t70) cc_final: 0.7384 (t70) REVERT: C 154 ASP cc_start: 0.7671 (m-30) cc_final: 0.7420 (m-30) REVERT: C 186 ASP cc_start: 0.7744 (m-30) cc_final: 0.7487 (m-30) REVERT: C 188 MET cc_start: 0.8144 (mmm) cc_final: 0.7857 (mmp) REVERT: C 254 ASP cc_start: 0.7509 (t0) cc_final: 0.7259 (t0) REVERT: C 273 ILE cc_start: 0.7864 (mm) cc_final: 0.7632 (mm) REVERT: C 304 ARG cc_start: 0.8568 (ttp80) cc_final: 0.8254 (ttp80) outliers start: 20 outliers final: 17 residues processed: 160 average time/residue: 1.2834 time to fit residues: 216.1801 Evaluate side-chains 170 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain D residue 6 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 25 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 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 246 ASN B 259 ASN B 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.139181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119992 restraints weight = 9600.974| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.12 r_work: 0.3384 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7366 Z= 0.253 Angle : 0.581 6.425 10021 Z= 0.310 Chirality : 0.043 0.234 1152 Planarity : 0.005 0.052 1276 Dihedral : 4.726 29.468 1000 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.69 % Allowed : 20.70 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.29), residues: 914 helix: 2.08 (0.26), residues: 407 sheet: -0.75 (0.38), residues: 170 loop : 0.00 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 169 HIS 0.003 0.001 HIS A 267 PHE 0.042 0.002 PHE A 43 TYR 0.020 0.001 TYR A 75 ARG 0.007 0.001 ARG B 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5658.52 seconds wall clock time: 100 minutes 21.87 seconds (6021.87 seconds total)