Starting phenix.real_space_refine on Wed Mar 12 14:58:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8q_37356/03_2025/8w8q_37356_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8q_37356/03_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_37356/03_2025/8w8q_37356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8q_37356/03_2025/8w8q_37356.map" model { file = "/net/cci-nas-00/data/ceres_data/8w8q_37356/03_2025/8w8q_37356_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8q_37356/03_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-5624/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: 5.23, per 1000 atoms: 0.64 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: 2.06 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: 1.08 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: 2.92 Time building geometry restraints manager: 2.49 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: 0.900 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.150 Find NCS groups from input model: 0.080 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:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.250 ------------------------------------------------------------------------------- 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 8342 Z= 0.330 Angle : 0.741 9.863 11321 Z= 0.492 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 *********************** 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 : 0.912 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: 1.2534 time to fit residues: 183.1255 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 : 0.805 ------------------------------------------------------------------------------- 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: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.126965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.093281 restraints weight = 11227.971| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.10 r_work: 0.2973 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8342 Z= 0.178 Angle : 0.537 7.590 11321 Z= 0.290 Chirality : 0.041 0.159 1292 Planarity : 0.004 0.043 1435 Dihedral : 4.812 53.027 1147 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.64 % Allowed : 20.16 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.25), residues: 1028 helix: 2.23 (0.25), residues: 411 sheet: 0.59 (0.33), residues: 222 loop : -0.53 (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 0.013 0.001 PHE A 376 TYR 0.013 0.001 TYR C 454 ARG 0.004 0.000 ARG N 72 *********************** 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 162 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.974 Fit side-chains REVERT: C 61 GLN cc_start: 0.7331 (mt0) cc_final: 0.6958 (tp40) REVERT: C 96 PHE cc_start: 0.6296 (m-80) cc_final: 0.5675 (t80) REVERT: C 424 TRP cc_start: 0.6981 (m100) cc_final: 0.6718 (m-90) REVERT: A 221 MET cc_start: 0.8950 (ttp) cc_final: 0.8457 (ttp) REVERT: B 59 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8574 (t80) REVERT: B 198 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8367 (pp) REVERT: B 262 MET cc_start: 0.9190 (mtp) cc_final: 0.8728 (mmm) outliers start: 32 outliers final: 13 residues processed: 155 average time/residue: 1.1704 time to fit residues: 193.2514 Evaluate side-chains 131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 2 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 B 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091635 restraints weight = 11431.393| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.13 r_work: 0.2956 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8342 Z= 0.194 Angle : 0.522 7.521 11321 Z= 0.281 Chirality : 0.042 0.160 1292 Planarity : 0.004 0.046 1435 Dihedral : 4.587 52.934 1139 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.87 % Allowed : 21.18 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1028 helix: 2.31 (0.24), residues: 411 sheet: 0.44 (0.32), residues: 227 loop : -0.46 (0.29), residues: 390 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 0.012 0.001 TYR A 339 ARG 0.003 0.000 ARG N 72 *********************** 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 159 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.887 Fit side-chains REVERT: C 61 GLN cc_start: 0.7344 (mt0) cc_final: 0.6980 (tp-100) REVERT: C 96 PHE cc_start: 0.6240 (m-80) cc_final: 0.5551 (t80) REVERT: C 147 ARG cc_start: 0.7813 (ttm170) cc_final: 0.7501 (tpp80) REVERT: C 440 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7388 (mp) REVERT: C 473 PHE cc_start: 0.5906 (OUTLIER) cc_final: 0.5693 (t80) REVERT: A 221 MET cc_start: 0.9102 (ttp) cc_final: 0.8618 (ttp) REVERT: B 59 TYR cc_start: 0.9146 (OUTLIER) cc_final: 0.8531 (t80) REVERT: B 198 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8349 (pp) REVERT: B 262 MET cc_start: 0.9125 (mtp) cc_final: 0.8821 (mmm) REVERT: G 20 LYS cc_start: 0.8473 (ttmm) cc_final: 0.7943 (mttp) REVERT: G 42 GLU cc_start: 0.8249 (pp20) cc_final: 0.7970 (tm-30) outliers start: 34 outliers final: 14 residues processed: 149 average time/residue: 1.2049 time to fit residues: 190.6718 Evaluate side-chains 131 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 65 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 91 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.125750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.092015 restraints weight = 11402.663| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.11 r_work: 0.2949 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8342 Z= 0.198 Angle : 0.515 7.433 11321 Z= 0.278 Chirality : 0.041 0.163 1292 Planarity : 0.004 0.046 1435 Dihedral : 4.598 53.973 1139 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.13 % Allowed : 20.96 % Favored : 73.92 % 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 (0.25), residues: 1028 helix: 2.33 (0.24), residues: 411 sheet: 0.40 (0.33), residues: 227 loop : -0.43 (0.30), 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 0.012 0.001 TYR N 95 ARG 0.004 0.000 ARG A 283 *********************** 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 167 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.936 Fit side-chains REVERT: C 61 GLN cc_start: 0.7370 (mt0) cc_final: 0.7074 (tp40) REVERT: C 96 PHE cc_start: 0.6248 (m-80) cc_final: 0.5538 (t80) REVERT: C 147 ARG cc_start: 0.7823 (ttm170) cc_final: 0.7491 (tpp80) REVERT: C 440 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7383 (mp) REVERT: C 473 PHE cc_start: 0.5907 (OUTLIER) cc_final: 0.5696 (t80) REVERT: A 221 MET cc_start: 0.9073 (ttp) cc_final: 0.8616 (ttp) REVERT: B 31 SER cc_start: 0.8191 (m) cc_final: 0.7924 (t) REVERT: B 59 TYR cc_start: 0.9134 (OUTLIER) cc_final: 0.8526 (t80) REVERT: B 198 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8350 (pp) REVERT: B 262 MET cc_start: 0.9090 (mtp) cc_final: 0.8878 (mtp) REVERT: N 43 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7870 (mttt) outliers start: 45 outliers final: 21 residues processed: 155 average time/residue: 1.1503 time to fit residues: 189.6832 Evaluate side-chains 143 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR 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 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 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: 0.7980 chunk 96 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 61 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- 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 ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.093751 restraints weight = 11313.817| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.11 r_work: 0.2985 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8342 Z= 0.151 Angle : 0.504 7.121 11321 Z= 0.268 Chirality : 0.041 0.151 1292 Planarity : 0.003 0.044 1435 Dihedral : 4.344 52.881 1137 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.78 % Allowed : 20.62 % Favored : 74.60 % 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: 1.33 (0.25), residues: 1028 helix: 2.38 (0.24), residues: 411 sheet: 0.36 (0.33), residues: 228 loop : -0.39 (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 0.023 0.001 PHE C 41 TYR 0.011 0.001 TYR N 95 ARG 0.003 0.000 ARG A 283 *********************** 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 : 0.876 Fit side-chains REVERT: C 61 GLN cc_start: 0.7304 (mt0) cc_final: 0.7060 (tp40) REVERT: C 96 PHE cc_start: 0.6253 (m-80) cc_final: 0.5506 (t80) REVERT: C 440 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7362 (mp) REVERT: C 473 PHE cc_start: 0.5911 (OUTLIER) cc_final: 0.5691 (t80) REVERT: A 221 MET cc_start: 0.9017 (ttp) cc_final: 0.8617 (ttp) REVERT: B 59 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8493 (t80) REVERT: B 198 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8336 (pp) REVERT: B 217 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7983 (pmm) REVERT: B 262 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8810 (mtp) REVERT: N 43 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7877 (mttt) outliers start: 42 outliers final: 20 residues processed: 151 average time/residue: 1.2525 time to fit residues: 200.9383 Evaluate side-chains 144 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 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 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 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 262 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.090633 restraints weight = 11333.410| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.10 r_work: 0.2930 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8342 Z= 0.267 Angle : 0.556 7.478 11321 Z= 0.299 Chirality : 0.043 0.178 1292 Planarity : 0.004 0.045 1435 Dihedral : 4.627 56.102 1137 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.13 % Allowed : 20.84 % 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: 1.27 (0.25), residues: 1028 helix: 2.26 (0.24), residues: 411 sheet: 0.50 (0.33), residues: 224 loop : -0.46 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.004 0.001 HIS C 223 PHE 0.022 0.002 PHE C 41 TYR 0.015 0.002 TYR A 339 ARG 0.002 0.000 ARG B 251 *********************** 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 170 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 125 time to evaluate : 1.093 Fit side-chains REVERT: C 61 GLN cc_start: 0.7331 (mt0) cc_final: 0.7067 (tp-100) REVERT: C 96 PHE cc_start: 0.6357 (m-80) cc_final: 0.5527 (t80) REVERT: C 147 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7539 (tpp80) REVERT: C 440 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7390 (mp) REVERT: C 473 PHE cc_start: 0.5905 (OUTLIER) cc_final: 0.5681 (t80) REVERT: A 221 MET cc_start: 0.9033 (ttp) cc_final: 0.8676 (ttp) REVERT: B 59 TYR cc_start: 0.9146 (OUTLIER) cc_final: 0.8554 (t80) REVERT: B 198 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8303 (pp) REVERT: B 217 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8081 (pmm) REVERT: B 262 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8833 (mtp) REVERT: B 314 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8527 (ptm160) REVERT: N 43 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7909 (mttt) outliers start: 45 outliers final: 22 residues processed: 157 average time/residue: 1.3155 time to fit residues: 220.3601 Evaluate side-chains 152 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 262 MET 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 19 LEU 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: 1.9990 chunk 88 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 43 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.090431 restraints weight = 11319.176| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.09 r_work: 0.2929 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8342 Z= 0.246 Angle : 0.557 7.300 11321 Z= 0.298 Chirality : 0.042 0.174 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.650 56.980 1137 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.67 % Allowed : 21.53 % 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: 1.24 (0.25), residues: 1028 helix: 2.25 (0.24), residues: 411 sheet: 0.45 (0.33), residues: 225 loop : -0.48 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS B 311 PHE 0.023 0.001 PHE C 41 TYR 0.014 0.001 TYR A 339 ARG 0.004 0.000 ARG B 251 *********************** 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 166 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.852 Fit side-chains REVERT: C 61 GLN cc_start: 0.7349 (mt0) cc_final: 0.7120 (tp-100) REVERT: C 96 PHE cc_start: 0.6415 (m-80) cc_final: 0.5524 (t80) REVERT: C 440 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7357 (mp) REVERT: C 473 PHE cc_start: 0.5885 (OUTLIER) cc_final: 0.5681 (t80) REVERT: A 221 MET cc_start: 0.9026 (ttp) cc_final: 0.8653 (ttp) REVERT: B 59 TYR cc_start: 0.9175 (OUTLIER) cc_final: 0.8583 (t80) REVERT: B 198 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8305 (pp) REVERT: B 217 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7940 (pmm) REVERT: B 262 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8745 (mtp) REVERT: B 314 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8541 (ptm160) REVERT: G 42 GLU cc_start: 0.8248 (pp20) cc_final: 0.7954 (tm-30) REVERT: N 43 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7922 (mttt) outliers start: 41 outliers final: 24 residues processed: 152 average time/residue: 1.2949 time to fit residues: 207.9920 Evaluate side-chains 148 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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 A residue 386 MET 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 262 MET 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 19 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 A 31 GLN A 294 GLN B 9 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.088754 restraints weight = 11513.738| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.11 r_work: 0.2895 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8342 Z= 0.329 Angle : 0.604 7.662 11321 Z= 0.325 Chirality : 0.044 0.162 1292 Planarity : 0.005 0.046 1435 Dihedral : 4.893 59.144 1137 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.01 % Allowed : 21.41 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1028 helix: 2.09 (0.24), residues: 411 sheet: 0.43 (0.33), residues: 225 loop : -0.53 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 441 HIS 0.005 0.001 HIS B 311 PHE 0.022 0.002 PHE C 41 TYR 0.018 0.002 TYR A 339 ARG 0.003 0.000 ARG C 129 *********************** 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 167 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.868 Fit side-chains REVERT: C 46 PHE cc_start: 0.8204 (t80) cc_final: 0.7864 (t80) REVERT: C 61 GLN cc_start: 0.7369 (mt0) cc_final: 0.7167 (tp-100) REVERT: C 96 PHE cc_start: 0.6494 (m-80) cc_final: 0.5459 (t80) REVERT: A 221 MET cc_start: 0.9004 (ttp) cc_final: 0.8727 (ttp) REVERT: B 59 TYR cc_start: 0.9216 (OUTLIER) cc_final: 0.8649 (t80) REVERT: B 198 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8300 (pp) REVERT: B 217 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8059 (pmm) REVERT: B 262 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8833 (mtp) REVERT: G 42 GLU cc_start: 0.8276 (pp20) cc_final: 0.7958 (tm-30) outliers start: 44 outliers final: 25 residues processed: 153 average time/residue: 1.1983 time to fit residues: 194.5387 Evaluate side-chains 146 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 A residue 386 MET 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 262 MET 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 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 19 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 36 optimal weight: 6.9990 chunk 76 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 79 optimal weight: 0.0060 chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 40 optimal weight: 0.0060 chunk 68 optimal weight: 4.9990 overall best weight: 0.4214 ------------------------------------------------------------------------------- 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 B 9 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.126875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093384 restraints weight = 11479.197| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.12 r_work: 0.2963 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8342 Z= 0.158 Angle : 0.540 7.225 11321 Z= 0.287 Chirality : 0.041 0.150 1292 Planarity : 0.004 0.058 1435 Dihedral : 4.472 56.759 1137 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.08 % Allowed : 24.37 % Favored : 72.55 % 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: 2.31 (0.25), residues: 411 sheet: 0.41 (0.33), residues: 221 loop : -0.48 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 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 C 168 ARG 0.002 0.000 ARG B 251 *********************** 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 149 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.240 Fit side-chains REVERT: C 96 PHE cc_start: 0.6315 (m-80) cc_final: 0.5318 (t80) REVERT: C 424 TRP cc_start: 0.7186 (m100) cc_final: 0.6760 (m-90) REVERT: C 463 LYS cc_start: 0.8903 (tppt) cc_final: 0.8573 (tppt) REVERT: A 221 MET cc_start: 0.8961 (ttp) cc_final: 0.8685 (ttp) REVERT: B 59 TYR cc_start: 0.9131 (OUTLIER) cc_final: 0.8563 (t80) REVERT: B 217 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8000 (pmm) REVERT: B 262 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8717 (mtp) outliers start: 27 outliers final: 14 residues processed: 141 average time/residue: 1.3781 time to fit residues: 205.9956 Evaluate side-chains 132 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR 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 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 B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 262 MET 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 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: 4.9990 chunk 99 optimal weight: 0.0170 chunk 43 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN C 223 HIS A 31 GLN B 9 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.090979 restraints weight = 11333.085| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.10 r_work: 0.2943 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8342 Z= 0.243 Angle : 0.584 8.241 11321 Z= 0.311 Chirality : 0.043 0.152 1292 Planarity : 0.004 0.055 1435 Dihedral : 4.513 57.516 1134 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.39 % Allowed : 26.08 % Favored : 71.53 % 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: 2.23 (0.24), residues: 411 sheet: 0.48 (0.33), residues: 221 loop : -0.47 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 441 HIS 0.004 0.001 HIS C 223 PHE 0.023 0.001 PHE C 41 TYR 0.013 0.001 TYR A 339 ARG 0.003 0.000 ARG B 314 ********************** 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 136 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.874 Fit side-chains REVERT: C 59 LYS cc_start: 0.7711 (mppt) cc_final: 0.7032 (mmmt) REVERT: C 96 PHE cc_start: 0.6283 (m-80) cc_final: 0.5363 (t80) REVERT: C 463 LYS cc_start: 0.8912 (tppt) cc_final: 0.8582 (tppt) REVERT: A 221 MET cc_start: 0.8873 (ttp) cc_final: 0.8610 (ttp) REVERT: B 59 TYR cc_start: 0.9160 (OUTLIER) cc_final: 0.8587 (t80) REVERT: B 217 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8010 (pmm) REVERT: B 262 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8737 (mtp) outliers start: 21 outliers final: 17 residues processed: 130 average time/residue: 1.2115 time to fit residues: 167.1187 Evaluate side-chains 133 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 93 VAL 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 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 B residue 59 TYR 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 262 MET 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 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: 0.8980 chunk 83 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 0.0770 chunk 90 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.125558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.092062 restraints weight = 11505.095| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.11 r_work: 0.2952 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8342 Z= 0.189 Angle : 0.575 12.536 11321 Z= 0.306 Chirality : 0.042 0.146 1292 Planarity : 0.004 0.056 1435 Dihedral : 4.423 56.791 1134 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.73 % Allowed : 26.20 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.25), residues: 1028 helix: 2.27 (0.24), residues: 411 sheet: 0.41 (0.34), residues: 216 loop : -0.45 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 441 HIS 0.004 0.001 HIS C 223 PHE 0.024 0.001 PHE C 41 TYR 0.011 0.001 TYR N 95 ARG 0.002 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6498.53 seconds wall clock time: 113 minutes 1.61 seconds (6781.61 seconds total)