Starting phenix.real_space_refine on Fri Jun 6 17:19:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8q_37356/06_2025/8w8q_37356_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8q_37356/06_2025/8w8q_37356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w8q_37356/06_2025/8w8q_37356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8q_37356/06_2025/8w8q_37356.map" model { file = "/net/cci-nas-00/data/ceres_data/8w8q_37356/06_2025/8w8q_37356_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8q_37356/06_2025/8w8q_37356_neut.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 49 5.16 5 C 5209 2.51 5 N 1417 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8168 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2283 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1898 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2579 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.06, per 1000 atoms: 0.62 Number of scatterers: 8168 At special positions: 0 Unit cell: (77.848, 124.136, 92.576, 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 49 16.00 O 1493 8.00 N 1417 7.00 C 5209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 104 " - pdb=" SG CYS C 182 " 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: 1.92 Conformation dependent library (CDL) restraints added in 1.2 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 42.9% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'C' and resid 27 through 59 removed outlier: 3.591A pdb=" N LYS C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 93 removed outlier: 3.732A pdb=" N PHE C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 100 through 135 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 168 Proline residue: C 165 - end of helix Processing helix chain 'C' and resid 189 through 201 Processing helix chain 'C' and resid 201 through 228 Processing helix chain 'C' and resid 394 through 425 Proline residue: C 414 - end of helix Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.904A pdb=" N GLN C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 445 removed outlier: 3.637A pdb=" N ILE C 436 " --> pdb=" O PRO C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 455 Proline residue: C 451 - end of helix Processing helix chain 'C' and resid 458 through 473 Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.573A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.540A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.538A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.615A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.194A 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 3 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.645A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 174 through 176 removed outlier: 3.585A pdb=" N SER C 183 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP C 176 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU C 181 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.404A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.425A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.512A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.559A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 135 " --> 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 CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.614A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.600A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.163A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.324A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1269 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: 2.69 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2098 1.33 - 1.45: 1585 1.45 - 1.57: 4592 1.57 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 8342 Sorted by residual: bond pdb=" C CYS B 233 " pdb=" N PHE B 234 " ideal model delta sigma weight residual 1.331 1.231 0.099 1.41e-02 5.03e+03 4.94e+01 bond pdb=" N ILE B 37 " pdb=" CA ILE B 37 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.32e-02 5.74e+03 1.01e+01 bond pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.26e+00 bond pdb=" N VAL B 112 " pdb=" CA VAL B 112 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 8.96e+00 bond pdb=" N ILE B 232 " pdb=" CA ILE B 232 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.17e-02 7.31e+03 8.59e+00 ... (remaining 8337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 10931 1.97 - 3.95: 350 3.95 - 5.92: 35 5.92 - 7.89: 3 7.89 - 9.86: 2 Bond angle restraints: 11321 Sorted by residual: angle pdb=" CA THR B 274 " pdb=" CB THR B 274 " pdb=" OG1 THR B 274 " ideal model delta sigma weight residual 109.60 99.74 9.86 1.50e+00 4.44e-01 4.32e+01 angle pdb=" C CYS B 233 " pdb=" N PHE B 234 " pdb=" CA PHE B 234 " ideal model delta sigma weight residual 121.50 129.91 -8.41 1.43e+00 4.89e-01 3.46e+01 angle pdb=" N ASP A 284 " pdb=" CA ASP A 284 " pdb=" C ASP A 284 " ideal model delta sigma weight residual 113.30 106.71 6.59 1.34e+00 5.57e-01 2.42e+01 angle pdb=" O ASP B 247 " pdb=" C ASP B 247 " pdb=" N ALA B 248 " ideal model delta sigma weight residual 122.39 127.12 -4.73 1.29e+00 6.01e-01 1.34e+01 angle pdb=" C ASP B 298 " pdb=" CA ASP B 298 " pdb=" CB ASP B 298 " ideal model delta sigma weight residual 109.89 115.50 -5.61 1.60e+00 3.91e-01 1.23e+01 ... (remaining 11316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 4364 17.17 - 34.34: 445 34.34 - 51.51: 122 51.51 - 68.67: 27 68.67 - 85.84: 4 Dihedral angle restraints: 4962 sinusoidal: 1918 harmonic: 3044 Sorted by residual: dihedral pdb=" CA ILE C 201 " pdb=" C ILE C 201 " pdb=" N VAL C 202 " pdb=" CA VAL C 202 " ideal model delta harmonic sigma weight residual 180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLU B 215 " pdb=" C GLU B 215 " pdb=" N GLY B 216 " pdb=" CA GLY B 216 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 65.31 27.69 1 1.00e+01 1.00e-02 1.10e+01 ... (remaining 4959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1007 0.052 - 0.103: 204 0.103 - 0.155: 57 0.155 - 0.207: 17 0.207 - 0.258: 7 Chirality restraints: 1292 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA LEU B 146 " pdb=" N LEU B 146 " pdb=" C LEU B 146 " pdb=" CB LEU B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1289 not shown) Planarity restraints: 1435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 29 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C ALA C 29 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA C 29 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS C 30 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 40 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ILE C 40 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE C 40 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE C 41 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 413 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO C 414 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 414 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 414 " 0.023 5.00e-02 4.00e+02 ... (remaining 1432 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1068 2.75 - 3.29: 7912 3.29 - 3.83: 14110 3.83 - 4.36: 16957 4.36 - 4.90: 29011 Nonbonded interactions: 69058 Sorted by model distance: nonbonded pdb=" O PHE C 200 " pdb=" OH TYR C 408 " model vdw 2.216 3.040 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.255 3.120 nonbonded pdb=" N GLU G 58 " pdb=" OE1 GLU G 58 " model vdw 2.259 3.120 nonbonded pdb=" O MET C 143 " pdb=" NH2 ARG A 38 " model vdw 2.281 3.120 nonbonded pdb=" O VAL C 88 " pdb=" OG1 THR C 91 " model vdw 2.290 3.040 ... (remaining 69053 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: 0.860 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.520 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 0.099 8345 Z= 0.355 Angle : 0.741 9.863 11327 Z= 0.491 Chirality : 0.051 0.258 1292 Planarity : 0.004 0.041 1435 Dihedral : 15.287 85.843 2981 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.71 % Allowed : 21.53 % Favored : 76.77 % 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: 1.04 (0.25), residues: 1028 helix: 1.98 (0.25), residues: 407 sheet: 0.61 (0.33), residues: 219 loop : -0.60 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 297 HIS 0.006 0.001 HIS C 223 PHE 0.011 0.001 PHE A 376 TYR 0.015 0.001 TYR C 454 ARG 0.003 0.000 ARG C 146 Details of bonding type rmsd hydrogen bonds : bond 0.16202 ( 440) hydrogen bonds : angle 6.02101 ( 1269) SS BOND : bond 0.00057 ( 3) SS BOND : angle 0.40255 ( 6) covalent geometry : bond 0.00513 ( 8342) covalent geometry : angle 0.74139 (11321) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.897 Fit side-chains REVERT: C 61 GLN cc_start: 0.7222 (mt0) cc_final: 0.6987 (tp40) REVERT: C 96 PHE cc_start: 0.6225 (m-80) cc_final: 0.5766 (t80) REVERT: C 183 SER cc_start: 0.8282 (t) cc_final: 0.7815 (p) REVERT: C 464 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7416 (mt-10) REVERT: A 53 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8130 (ttmm) REVERT: A 221 MET cc_start: 0.8966 (ttp) cc_final: 0.8424 (ttp) REVERT: B 59 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8429 (t80) outliers start: 15 outliers final: 5 residues processed: 138 average time/residue: 1.2304 time to fit residues: 179.6898 Evaluate side-chains 121 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN C 222 GLN C 223 HIS A 294 GLN A 357 HIS A 371 ASN B 9 GLN B 32 GLN B 88 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092914 restraints weight = 11238.975| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.10 r_work: 0.2967 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8345 Z= 0.130 Angle : 0.535 7.581 11327 Z= 0.290 Chirality : 0.041 0.159 1292 Planarity : 0.004 0.043 1435 Dihedral : 4.804 53.087 1147 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.87 % Allowed : 20.05 % Favored : 76.08 % 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: 1.25 (0.25), residues: 1028 helix: 2.24 (0.25), residues: 411 sheet: 0.59 (0.33), residues: 222 loop : -0.52 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 PHE 0.014 0.001 PHE C 41 TYR 0.013 0.001 TYR C 454 ARG 0.004 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.05027 ( 440) hydrogen bonds : angle 4.70098 ( 1269) SS BOND : bond 0.00135 ( 3) SS BOND : angle 0.31031 ( 6) covalent geometry : bond 0.00280 ( 8342) covalent geometry : angle 0.53559 (11321) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.977 Fit side-chains REVERT: C 61 GLN cc_start: 0.7297 (mt0) cc_final: 0.6938 (tp40) REVERT: C 96 PHE cc_start: 0.6312 (m-80) cc_final: 0.5660 (t80) REVERT: C 424 TRP cc_start: 0.6978 (m100) cc_final: 0.6698 (m-90) REVERT: A 221 MET cc_start: 0.8976 (ttp) cc_final: 0.8483 (ttp) REVERT: B 59 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8568 (t80) REVERT: B 198 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8374 (pp) REVERT: B 217 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8201 (pmm) REVERT: B 262 MET cc_start: 0.9195 (mtp) cc_final: 0.8899 (mmm) outliers start: 34 outliers final: 13 residues processed: 155 average time/residue: 1.1620 time to fit residues: 191.5432 Evaluate side-chains 131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 51 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 91 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 31 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: C 222 GLN C 223 HIS A 357 HIS B 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.127087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.093540 restraints weight = 11398.098| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.11 r_work: 0.2979 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8345 Z= 0.118 Angle : 0.511 7.422 11327 Z= 0.274 Chirality : 0.041 0.162 1292 Planarity : 0.004 0.043 1435 Dihedral : 4.499 51.992 1139 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.76 % Allowed : 21.18 % Favored : 75.06 % 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 (0.25), residues: 1028 helix: 2.35 (0.24), residues: 411 sheet: 0.46 (0.32), residues: 224 loop : -0.46 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 PHE 0.025 0.001 PHE C 41 TYR 0.011 0.001 TYR N 95 ARG 0.003 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 440) hydrogen bonds : angle 4.49399 ( 1269) SS BOND : bond 0.00100 ( 3) SS BOND : angle 0.25190 ( 6) covalent geometry : bond 0.00252 ( 8342) covalent geometry : angle 0.51119 (11321) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.933 Fit side-chains REVERT: C 61 GLN cc_start: 0.7346 (mt0) cc_final: 0.7000 (tp40) REVERT: C 96 PHE cc_start: 0.6261 (m-80) cc_final: 0.5593 (t80) REVERT: C 440 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7337 (mp) REVERT: C 473 PHE cc_start: 0.5905 (OUTLIER) cc_final: 0.5689 (t80) REVERT: A 221 MET cc_start: 0.9097 (ttp) cc_final: 0.8586 (ttp) REVERT: B 59 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8562 (t80) REVERT: B 198 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8356 (pp) REVERT: G 20 LYS cc_start: 0.8469 (ttmm) cc_final: 0.7950 (mttp) outliers start: 33 outliers final: 13 residues processed: 148 average time/residue: 1.1460 time to fit residues: 180.5184 Evaluate side-chains 129 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 35 optimal weight: 0.1980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS A 29 GLN A 390 GLN B 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.092079 restraints weight = 11396.874| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.12 r_work: 0.2955 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8345 Z= 0.141 Angle : 0.518 7.434 11327 Z= 0.279 Chirality : 0.042 0.164 1292 Planarity : 0.004 0.043 1435 Dihedral : 4.485 53.826 1137 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.78 % Allowed : 20.96 % Favored : 74.26 % 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 (0.25), residues: 1028 helix: 2.37 (0.24), residues: 411 sheet: 0.40 (0.32), residues: 227 loop : -0.42 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 PHE 0.020 0.001 PHE C 41 TYR 0.013 0.001 TYR A 339 ARG 0.002 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 440) hydrogen bonds : angle 4.45918 ( 1269) SS BOND : bond 0.00100 ( 3) SS BOND : angle 0.34178 ( 6) covalent geometry : bond 0.00316 ( 8342) covalent geometry : angle 0.51833 (11321) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 120 time to evaluate : 0.995 Fit side-chains REVERT: C 61 GLN cc_start: 0.7393 (mt0) cc_final: 0.7068 (tp40) REVERT: C 96 PHE cc_start: 0.6238 (m-80) cc_final: 0.5545 (t80) REVERT: C 147 ARG cc_start: 0.7810 (ttm170) cc_final: 0.7471 (tpp80) REVERT: C 440 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7387 (mp) REVERT: C 473 PHE cc_start: 0.5910 (OUTLIER) cc_final: 0.5697 (t80) REVERT: A 221 MET cc_start: 0.9071 (ttp) cc_final: 0.8620 (ttp) REVERT: B 59 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.8519 (t80) REVERT: B 198 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8359 (pp) REVERT: N 43 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7870 (mttt) outliers start: 42 outliers final: 22 residues processed: 152 average time/residue: 1.1691 time to fit residues: 189.0487 Evaluate side-chains 142 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.9980 chunk 96 optimal weight: 0.4980 chunk 14 optimal weight: 0.0070 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS A 390 GLN B 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.091664 restraints weight = 11337.816| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.10 r_work: 0.2966 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8345 Z= 0.134 Angle : 0.520 7.318 11327 Z= 0.278 Chirality : 0.042 0.155 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.463 54.064 1137 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.78 % Allowed : 21.07 % Favored : 74.15 % 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: 1.31 (0.25), residues: 1028 helix: 2.36 (0.24), residues: 411 sheet: 0.35 (0.33), residues: 228 loop : -0.40 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 PHE 0.022 0.001 PHE C 41 TYR 0.012 0.001 TYR N 95 ARG 0.004 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04611 ( 440) hydrogen bonds : angle 4.42764 ( 1269) SS BOND : bond 0.00098 ( 3) SS BOND : angle 0.36137 ( 6) covalent geometry : bond 0.00300 ( 8342) covalent geometry : angle 0.52022 (11321) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 0.991 Fit side-chains REVERT: C 61 GLN cc_start: 0.7291 (mt0) cc_final: 0.7066 (tp40) REVERT: C 96 PHE cc_start: 0.6310 (m-80) cc_final: 0.5515 (t80) REVERT: C 147 ARG cc_start: 0.7797 (ttm170) cc_final: 0.7450 (tpp80) REVERT: C 440 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7358 (mp) REVERT: C 473 PHE cc_start: 0.5917 (OUTLIER) cc_final: 0.5691 (t80) REVERT: A 221 MET cc_start: 0.9057 (ttp) cc_final: 0.8643 (ttp) REVERT: B 31 SER cc_start: 0.8117 (m) cc_final: 0.7909 (t) REVERT: B 59 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8513 (t80) REVERT: B 198 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8353 (pp) REVERT: B 217 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8037 (pmm) REVERT: G 46 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8773 (mmtm) REVERT: N 43 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7855 (mttt) outliers start: 42 outliers final: 23 residues processed: 153 average time/residue: 1.3703 time to fit residues: 222.4419 Evaluate side-chains 148 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS B 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.092246 restraints weight = 11310.734| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.10 r_work: 0.2959 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8345 Z= 0.136 Angle : 0.522 7.321 11327 Z= 0.280 Chirality : 0.041 0.149 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.471 54.370 1137 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.90 % Allowed : 21.07 % Favored : 74.03 % 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: 1.29 (0.25), residues: 1028 helix: 2.35 (0.24), residues: 411 sheet: 0.32 (0.33), residues: 228 loop : -0.40 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 PHE 0.023 0.001 PHE C 41 TYR 0.012 0.001 TYR N 95 ARG 0.003 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04576 ( 440) hydrogen bonds : angle 4.41662 ( 1269) SS BOND : bond 0.00096 ( 3) SS BOND : angle 0.38368 ( 6) covalent geometry : bond 0.00308 ( 8342) covalent geometry : angle 0.52186 (11321) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.985 Fit side-chains REVERT: C 61 GLN cc_start: 0.7330 (mt0) cc_final: 0.7107 (tp40) REVERT: C 96 PHE cc_start: 0.6356 (m-80) cc_final: 0.5521 (t80) REVERT: C 147 ARG cc_start: 0.7811 (ttm170) cc_final: 0.7453 (tpp80) REVERT: C 440 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7342 (mp) REVERT: C 473 PHE cc_start: 0.5908 (OUTLIER) cc_final: 0.5689 (t80) REVERT: A 221 MET cc_start: 0.9028 (ttp) cc_final: 0.8646 (ttp) REVERT: B 59 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.8515 (t80) REVERT: B 198 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8329 (pp) REVERT: B 217 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7918 (pmm) REVERT: B 314 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8444 (ptm160) REVERT: N 43 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7865 (mttt) outliers start: 43 outliers final: 23 residues processed: 156 average time/residue: 1.3798 time to fit residues: 227.8230 Evaluate side-chains 149 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 7.9990 chunk 88 optimal weight: 0.0870 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS A 31 GLN A 294 GLN B 9 GLN N 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.092026 restraints weight = 11295.989| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.11 r_work: 0.2951 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8345 Z= 0.140 Angle : 0.533 7.336 11327 Z= 0.284 Chirality : 0.042 0.188 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.481 54.961 1137 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.56 % Allowed : 21.64 % Favored : 73.80 % 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: 1.32 (0.25), residues: 1028 helix: 2.37 (0.24), residues: 411 sheet: 0.33 (0.33), residues: 228 loop : -0.39 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS C 223 PHE 0.023 0.001 PHE C 41 TYR 0.014 0.001 TYR N 95 ARG 0.003 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 440) hydrogen bonds : angle 4.41913 ( 1269) SS BOND : bond 0.00092 ( 3) SS BOND : angle 0.40405 ( 6) covalent geometry : bond 0.00317 ( 8342) covalent geometry : angle 0.53265 (11321) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.741 Fit side-chains REVERT: C 61 GLN cc_start: 0.7285 (mt0) cc_final: 0.7065 (tp-100) REVERT: C 96 PHE cc_start: 0.6366 (m-80) cc_final: 0.5515 (t80) REVERT: C 440 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7340 (mp) REVERT: C 473 PHE cc_start: 0.5905 (OUTLIER) cc_final: 0.5682 (t80) REVERT: A 221 MET cc_start: 0.9010 (ttp) cc_final: 0.8647 (ttp) REVERT: B 3 GLU cc_start: 0.6664 (tm-30) cc_final: 0.6440 (tm-30) REVERT: B 59 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.8540 (t80) REVERT: B 198 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8303 (pp) REVERT: B 217 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8021 (pmm) REVERT: B 314 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8498 (ptm160) REVERT: N 43 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7874 (mttt) outliers start: 40 outliers final: 23 residues processed: 151 average time/residue: 1.3536 time to fit residues: 215.7998 Evaluate side-chains 148 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 63 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS C 458 HIS A 31 GLN A 294 GLN B 9 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.123016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.089163 restraints weight = 11490.296| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.10 r_work: 0.2916 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8345 Z= 0.193 Angle : 0.579 7.601 11327 Z= 0.311 Chirality : 0.043 0.174 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.735 57.590 1137 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.44 % Allowed : 22.67 % Favored : 72.89 % 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 (0.25), residues: 1028 helix: 2.24 (0.24), residues: 411 sheet: 0.43 (0.33), residues: 225 loop : -0.46 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 441 HIS 0.004 0.001 HIS C 223 PHE 0.022 0.002 PHE C 41 TYR 0.016 0.002 TYR A 339 ARG 0.003 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.04983 ( 440) hydrogen bonds : angle 4.55798 ( 1269) SS BOND : bond 0.00174 ( 3) SS BOND : angle 0.55800 ( 6) covalent geometry : bond 0.00445 ( 8342) covalent geometry : angle 0.57870 (11321) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.722 Fit side-chains REVERT: C 61 GLN cc_start: 0.7273 (mt0) cc_final: 0.7055 (tp-100) REVERT: C 96 PHE cc_start: 0.6435 (m-80) cc_final: 0.5463 (t80) REVERT: C 440 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7323 (mp) REVERT: C 463 LYS cc_start: 0.8914 (tppt) cc_final: 0.8580 (tppt) REVERT: C 473 PHE cc_start: 0.5908 (OUTLIER) cc_final: 0.5697 (t80) REVERT: A 221 MET cc_start: 0.9015 (ttp) cc_final: 0.8640 (ttp) REVERT: B 59 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8612 (t80) REVERT: B 198 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8310 (pp) REVERT: B 217 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.7943 (pmm) REVERT: B 314 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8603 (ptm160) REVERT: G 42 GLU cc_start: 0.8267 (pp20) cc_final: 0.7954 (tm-30) REVERT: N 43 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7909 (mttt) outliers start: 39 outliers final: 23 residues processed: 150 average time/residue: 1.2761 time to fit residues: 203.2699 Evaluate side-chains 146 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 36 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 HIS C 223 HIS C 433 GLN B 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.087911 restraints weight = 11651.480| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.12 r_work: 0.2881 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8345 Z= 0.260 Angle : 0.635 7.784 11327 Z= 0.343 Chirality : 0.046 0.174 1292 Planarity : 0.005 0.054 1435 Dihedral : 5.041 59.521 1137 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.21 % Allowed : 23.69 % Favored : 72.10 % 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: 0.98 (0.25), residues: 1028 helix: 1.98 (0.24), residues: 411 sheet: 0.39 (0.33), residues: 223 loop : -0.60 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 441 HIS 0.005 0.001 HIS B 311 PHE 0.021 0.002 PHE C 41 TYR 0.020 0.002 TYR A 339 ARG 0.004 0.001 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.05437 ( 440) hydrogen bonds : angle 4.77908 ( 1269) SS BOND : bond 0.00216 ( 3) SS BOND : angle 0.71644 ( 6) covalent geometry : bond 0.00606 ( 8342) covalent geometry : angle 0.63493 (11321) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.882 Fit side-chains REVERT: C 46 PHE cc_start: 0.8215 (t80) cc_final: 0.7885 (t80) REVERT: A 221 MET cc_start: 0.9013 (ttp) cc_final: 0.8745 (ttp) REVERT: B 3 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6662 (tm-30) REVERT: B 59 TYR cc_start: 0.9234 (OUTLIER) cc_final: 0.8722 (t80) REVERT: B 198 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8296 (pp) REVERT: B 217 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8079 (pmm) REVERT: G 42 GLU cc_start: 0.8301 (pp20) cc_final: 0.7975 (tm-30) outliers start: 37 outliers final: 21 residues processed: 151 average time/residue: 1.1823 time to fit residues: 189.8423 Evaluate side-chains 139 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS B 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.090885 restraints weight = 11319.730| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.09 r_work: 0.2935 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8345 Z= 0.141 Angle : 0.573 8.180 11327 Z= 0.307 Chirality : 0.042 0.164 1292 Planarity : 0.004 0.059 1435 Dihedral : 4.744 57.705 1137 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.85 % Allowed : 25.40 % Favored : 71.75 % 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: 1.14 (0.25), residues: 1028 helix: 2.17 (0.24), residues: 411 sheet: 0.33 (0.33), residues: 225 loop : -0.48 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS C 223 PHE 0.023 0.001 PHE C 41 TYR 0.011 0.001 TYR A 339 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 440) hydrogen bonds : angle 4.59745 ( 1269) SS BOND : bond 0.00123 ( 3) SS BOND : angle 0.50026 ( 6) covalent geometry : bond 0.00317 ( 8342) covalent geometry : angle 0.57283 (11321) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.917 Fit side-chains REVERT: C 61 GLN cc_start: 0.7536 (tp-100) cc_final: 0.7328 (tp-100) REVERT: C 463 LYS cc_start: 0.8893 (tppt) cc_final: 0.8565 (tppt) REVERT: C 473 PHE cc_start: 0.5888 (OUTLIER) cc_final: 0.5685 (t80) REVERT: B 59 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8592 (t80) REVERT: B 198 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8289 (pp) REVERT: B 217 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8036 (pmm) outliers start: 25 outliers final: 19 residues processed: 134 average time/residue: 1.3461 time to fit residues: 191.6620 Evaluate side-chains 136 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 79 optimal weight: 0.0470 chunk 14 optimal weight: 0.6980 chunk 90 optimal weight: 0.0980 chunk 76 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS B 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.126092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092709 restraints weight = 11462.311| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.11 r_work: 0.2963 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8345 Z= 0.128 Angle : 0.553 7.876 11327 Z= 0.297 Chirality : 0.041 0.164 1292 Planarity : 0.004 0.058 1435 Dihedral : 4.539 56.447 1137 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.85 % Allowed : 25.51 % Favored : 71.64 % 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 (0.26), residues: 1028 helix: 2.31 (0.25), residues: 411 sheet: 0.42 (0.34), residues: 213 loop : -0.43 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS C 223 PHE 0.024 0.001 PHE C 41 TYR 0.010 0.001 TYR N 95 ARG 0.002 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 440) hydrogen bonds : angle 4.46969 ( 1269) SS BOND : bond 0.00100 ( 3) SS BOND : angle 0.43368 ( 6) covalent geometry : bond 0.00286 ( 8342) covalent geometry : angle 0.55329 (11321) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6570.95 seconds wall clock time: 114 minutes 47.54 seconds (6887.54 seconds total)