Starting phenix.real_space_refine on Sat Aug 3 11:18:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/08_2024/8kh5_37237.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/08_2024/8kh5_37237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/08_2024/8kh5_37237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/08_2024/8kh5_37237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/08_2024/8kh5_37237.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kh5_37237/08_2024/8kh5_37237.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.143 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 57 5.16 5 C 5034 2.51 5 N 1339 2.21 5 O 1407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2214 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1778 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 338, 2460 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 116 Conformer: "B" Number of residues, atoms: 338, 2460 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 116 bond proxies already assigned to first conformer: 2496 Chain: "E" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 946 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 345 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'CLR': 2, 'LPS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.15, per 1000 atoms: 0.78 Number of scatterers: 7838 At special positions: 0 Unit cell: (74.52, 97.2, 130.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 1 15.00 O 1407 8.00 N 1339 7.00 C 5034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.04 Conformation dependent library (CDL) restraints added in 2.0 seconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 43.3% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 15 through 51 removed outlier: 4.321A pdb=" N VAL A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 55 through 82 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 87 through 122 removed outlier: 3.630A pdb=" N LYS A 98 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 133 through 149 removed outlier: 3.526A pdb=" N CYS A 146 " --> pdb=" O TRP A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.699A pdb=" N LEU A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 213 Proline residue: A 197 - end of helix Processing helix chain 'A' and resid 223 through 258 removed outlier: 3.623A pdb=" N LEU A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Proline residue: A 245 - end of helix Proline residue: A 251 - end of helix Processing helix chain 'A' and resid 263 through 294 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'B' and resid 13 through 39 removed outlier: 3.595A pdb=" N ALA B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 39 " --> pdb=" O GLN B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 265 through 279 Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 307 through 312 removed outlier: 4.002A pdb=" N TYR B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'B' and resid 331 through 352 removed outlier: 3.651A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 391 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.692A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 removed outlier: 3.836A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'B' and resid 209 through 214 removed outlier: 3.912A pdb=" N ALA B 243 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE B 244 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N PHE B 290 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE B 246 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN B 292 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 248 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.730A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.818A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.085A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.529A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.636A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.482A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 254 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.759A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.046A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1290 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: 2.16 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1234 1.30 - 1.43: 2168 1.43 - 1.55: 4530 1.55 - 1.68: 4 1.68 - 1.81: 78 Bond restraints: 8014 Sorted by residual: bond pdb=" C PRO A 123 " pdb=" O PRO A 123 " ideal model delta sigma weight residual 1.237 1.410 -0.173 1.26e-02 6.30e+03 1.88e+02 bond pdb=" C31 LPS A 402 " pdb=" O32 LPS A 402 " ideal model delta sigma weight residual 1.398 1.180 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CA ALA A 140 " pdb=" C ALA A 140 " ideal model delta sigma weight residual 1.524 1.412 0.112 1.29e-02 6.01e+03 7.53e+01 bond pdb=" C ASP A 16 " pdb=" O ASP A 16 " ideal model delta sigma weight residual 1.235 1.314 -0.079 1.26e-02 6.30e+03 3.94e+01 bond pdb=" C PHE A 126 " pdb=" O PHE A 126 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.15e-02 7.56e+03 3.44e+01 ... (remaining 8009 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.44: 205 106.44 - 113.34: 4419 113.34 - 120.23: 2786 120.23 - 127.13: 3433 127.13 - 134.03: 84 Bond angle restraints: 10927 Sorted by residual: angle pdb=" N PHE A 126 " pdb=" CA PHE A 126 " pdb=" C PHE A 126 " ideal model delta sigma weight residual 111.07 123.34 -12.27 1.07e+00 8.73e-01 1.32e+02 angle pdb=" N CYS A 129 " pdb=" CA CYS A 129 " pdb=" C CYS A 129 " ideal model delta sigma weight residual 112.92 100.41 12.51 1.23e+00 6.61e-01 1.03e+02 angle pdb=" N LYS A 130 " pdb=" CA LYS A 130 " pdb=" C LYS A 130 " ideal model delta sigma weight residual 112.57 102.29 10.28 1.13e+00 7.83e-01 8.28e+01 angle pdb=" CA PHE A 126 " pdb=" C PHE A 126 " pdb=" N HIS A 127 " ideal model delta sigma weight residual 117.07 126.17 -9.10 1.14e+00 7.69e-01 6.37e+01 angle pdb=" O PHE A 126 " pdb=" C PHE A 126 " pdb=" N HIS A 127 " ideal model delta sigma weight residual 122.07 114.52 7.55 1.03e+00 9.43e-01 5.37e+01 ... (remaining 10922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 4301 15.07 - 30.14: 382 30.14 - 45.21: 103 45.21 - 60.29: 19 60.29 - 75.36: 8 Dihedral angle restraints: 4813 sinusoidal: 1799 harmonic: 3014 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 147.71 -54.71 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" N PHE A 124 " pdb=" C PHE A 124 " pdb=" CA PHE A 124 " pdb=" CB PHE A 124 " ideal model delta harmonic sigma weight residual 122.80 110.88 11.92 0 2.50e+00 1.60e-01 2.27e+01 dihedral pdb=" CB CYS A 91 " pdb=" SG CYS A 91 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 131.85 -38.85 1 1.00e+01 1.00e-02 2.12e+01 ... (remaining 4810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.443: 1274 0.443 - 0.886: 1 0.886 - 1.329: 0 1.329 - 1.772: 0 1.772 - 2.214: 1 Chirality restraints: 1276 Sorted by residual: chirality pdb=" C31 LPS A 402 " pdb=" C32 LPS A 402 " pdb=" O31 LPS A 402 " pdb=" O32 LPS A 402 " both_signs ideal model delta sigma weight residual False -2.18 0.04 -2.21 2.00e-01 2.50e+01 1.23e+02 chirality pdb=" CA PHE A 126 " pdb=" N PHE A 126 " pdb=" C PHE A 126 " pdb=" CB PHE A 126 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.49e+00 chirality pdb=" C13 CLR A 401 " pdb=" C12 CLR A 401 " pdb=" C14 CLR A 401 " pdb=" C17 CLR A 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.52 -0.41 2.00e-01 2.50e+01 4.14e+00 ... (remaining 1273 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 124 " 0.025 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C PHE A 124 " -0.085 2.00e-02 2.50e+03 pdb=" O PHE A 124 " 0.031 2.00e-02 2.50e+03 pdb=" N ARG A 125 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 126 " -0.025 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C PHE A 126 " 0.081 2.00e-02 2.50e+03 pdb=" O PHE A 126 " -0.028 2.00e-02 2.50e+03 pdb=" N HIS A 127 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 122 " -0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 123 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.032 5.00e-02 4.00e+02 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 134 2.66 - 3.22: 7451 3.22 - 3.78: 12640 3.78 - 4.34: 17575 4.34 - 4.90: 29164 Nonbonded interactions: 66964 Sorted by model distance: nonbonded pdb=" OD1 ASP E 50 " pdb=" OG SER E 59 " model vdw 2.103 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.189 3.040 nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 171 " model vdw 2.197 3.040 nonbonded pdb=" NH1 ARG B 228 " pdb=" OD1 ASP C 186 " model vdw 2.249 3.120 nonbonded pdb=" O CYS C 149 " pdb=" NH1 ARG C 150 " model vdw 2.254 3.120 ... (remaining 66959 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=0.45 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 26.110 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 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 : 0.008 0.218 8014 Z= 0.503 Angle : 0.852 17.124 10927 Z= 0.505 Chirality : 0.084 2.214 1276 Planarity : 0.005 0.060 1371 Dihedral : 12.854 75.356 2856 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.26 % Allowed : 0.77 % Favored : 98.97 % Cbeta Deviations : 0.10 % 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: 0.90 (0.27), residues: 1018 helix: 1.86 (0.27), residues: 402 sheet: 0.40 (0.34), residues: 218 loop : -0.56 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 142 HIS 0.011 0.002 HIS C 142 PHE 0.028 0.002 PHE A 239 TYR 0.031 0.002 TYR C 59 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 118 TRP cc_start: 0.6917 (t-100) cc_final: 0.6332 (t60) REVERT: A 250 PHE cc_start: 0.7690 (t80) cc_final: 0.7479 (t80) REVERT: B 317 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7440 (mtm-85) REVERT: B 378 ASP cc_start: 0.7929 (m-30) cc_final: 0.7619 (m-30) REVERT: C 277 SER cc_start: 0.8496 (t) cc_final: 0.8110 (m) outliers start: 2 outliers final: 2 residues processed: 206 average time/residue: 0.9866 time to fit residues: 216.9097 Evaluate side-chains 134 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain B residue 229 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN B 213 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS C 119 ASN C 156 GLN C 175 GLN C 176 GLN C 220 GLN C 259 GLN E 31 ASN D 44 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8014 Z= 0.265 Angle : 0.611 7.708 10927 Z= 0.323 Chirality : 0.045 0.159 1276 Planarity : 0.005 0.059 1371 Dihedral : 7.141 107.944 1276 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.09 % Allowed : 11.20 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1018 helix: 1.92 (0.26), residues: 420 sheet: 0.54 (0.32), residues: 209 loop : -0.54 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 84 HIS 0.011 0.002 HIS B 220 PHE 0.027 0.002 PHE A 119 TYR 0.017 0.002 TYR C 59 ARG 0.009 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 118 TRP cc_start: 0.7514 (t-100) cc_final: 0.7136 (t-100) REVERT: A 185 MET cc_start: 0.7632 (tmm) cc_final: 0.7396 (tmm) REVERT: A 224 GLU cc_start: 0.7775 (mp0) cc_final: 0.7574 (mp0) REVERT: A 300 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7752 (mtp180) REVERT: A 301 ARG cc_start: 0.7327 (mtm-85) cc_final: 0.6863 (mtm-85) REVERT: B 274 LYS cc_start: 0.7770 (tttt) cc_final: 0.7508 (ttpt) REVERT: B 280 ARG cc_start: 0.7822 (ttt-90) cc_final: 0.7518 (ttt-90) REVERT: B 310 ASP cc_start: 0.7967 (t0) cc_final: 0.7628 (m-30) REVERT: B 317 ARG cc_start: 0.7753 (mtm-85) cc_final: 0.7511 (mtm-85) REVERT: C 197 ARG cc_start: 0.7055 (mtp-110) cc_final: 0.6727 (mtp85) REVERT: C 214 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.6310 (mpp80) REVERT: C 277 SER cc_start: 0.8425 (t) cc_final: 0.8072 (m) REVERT: E 80 TYR cc_start: 0.7138 (m-80) cc_final: 0.6585 (m-80) outliers start: 24 outliers final: 7 residues processed: 162 average time/residue: 1.2262 time to fit residues: 209.9107 Evaluate side-chains 132 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN B 23 ASN B 213 GLN B 292 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 88 ASN C 175 GLN C 176 GLN C 220 GLN C 259 GLN E 31 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8014 Z= 0.194 Angle : 0.527 5.614 10927 Z= 0.283 Chirality : 0.042 0.138 1276 Planarity : 0.004 0.058 1371 Dihedral : 5.771 57.172 1272 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.09 % Allowed : 15.19 % Favored : 81.72 % 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: 1.20 (0.26), residues: 1018 helix: 2.17 (0.26), residues: 420 sheet: 0.55 (0.32), residues: 209 loop : -0.58 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 84 HIS 0.007 0.001 HIS A 127 PHE 0.028 0.002 PHE A 119 TYR 0.012 0.001 TYR C 59 ARG 0.005 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 145 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.6832 (mp) REVERT: A 179 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7420 (tp) REVERT: A 185 MET cc_start: 0.7597 (tmm) cc_final: 0.7304 (tmm) REVERT: A 224 GLU cc_start: 0.7702 (mp0) cc_final: 0.7419 (mp0) REVERT: A 296 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7627 (t) REVERT: A 300 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7769 (mtp180) REVERT: B 218 ASN cc_start: 0.8395 (m-40) cc_final: 0.8062 (m110) REVERT: B 274 LYS cc_start: 0.7814 (tttt) cc_final: 0.7499 (ttpt) REVERT: B 280 ARG cc_start: 0.7838 (ttt-90) cc_final: 0.7547 (ttt-90) REVERT: B 317 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7216 (ptp-110) REVERT: B 330 GLU cc_start: 0.8013 (tt0) cc_final: 0.7638 (tt0) REVERT: B 378 ASP cc_start: 0.8140 (m-30) cc_final: 0.7906 (m-30) REVERT: C 45 MET cc_start: 0.8532 (mtt) cc_final: 0.7914 (mtt) REVERT: C 197 ARG cc_start: 0.7088 (mtp-110) cc_final: 0.6764 (mtp85) REVERT: C 214 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.6327 (mpp80) REVERT: E 80 TYR cc_start: 0.7250 (m-80) cc_final: 0.6731 (m-80) outliers start: 24 outliers final: 3 residues processed: 148 average time/residue: 1.2319 time to fit residues: 193.9626 Evaluate side-chains 128 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 175 GLN C 176 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8014 Z= 0.187 Angle : 0.518 7.397 10927 Z= 0.276 Chirality : 0.042 0.137 1276 Planarity : 0.004 0.057 1371 Dihedral : 5.569 55.759 1272 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.32 % Allowed : 17.25 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.27), residues: 1018 helix: 2.26 (0.26), residues: 418 sheet: 0.45 (0.32), residues: 220 loop : -0.50 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.006 0.001 HIS B 357 PHE 0.028 0.002 PHE A 119 TYR 0.020 0.001 TYR C 59 ARG 0.007 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 0.860 Fit side-chains REVERT: A 92 MET cc_start: 0.6485 (tpp) cc_final: 0.6144 (mmt) REVERT: A 179 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7458 (tp) REVERT: A 185 MET cc_start: 0.7550 (tmm) cc_final: 0.7298 (tmm) REVERT: A 300 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7745 (mtp180) REVERT: B 211 LYS cc_start: 0.8524 (mttp) cc_final: 0.7798 (mttm) REVERT: B 213 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8377 (tm-30) REVERT: B 218 ASN cc_start: 0.8428 (m-40) cc_final: 0.8192 (m110) REVERT: B 274 LYS cc_start: 0.7843 (tttt) cc_final: 0.7511 (ttpt) REVERT: B 280 ARG cc_start: 0.7815 (ttt-90) cc_final: 0.7506 (ttt-90) REVERT: B 317 ARG cc_start: 0.7793 (mtm-85) cc_final: 0.7298 (ptp-110) REVERT: B 318 TYR cc_start: 0.8298 (t80) cc_final: 0.7943 (t80) REVERT: B 330 GLU cc_start: 0.8066 (tt0) cc_final: 0.7691 (tt0) REVERT: C 197 ARG cc_start: 0.7116 (mtp-110) cc_final: 0.6670 (mtp85) REVERT: C 214 ARG cc_start: 0.6675 (mpp80) cc_final: 0.6357 (mpp80) REVERT: E 87 LYS cc_start: 0.7288 (mtpt) cc_final: 0.7081 (ttmm) outliers start: 18 outliers final: 6 residues processed: 151 average time/residue: 1.1782 time to fit residues: 188.3551 Evaluate side-chains 137 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0470 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 175 GLN C 176 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8014 Z= 0.165 Angle : 0.499 6.304 10927 Z= 0.266 Chirality : 0.041 0.138 1276 Planarity : 0.004 0.056 1371 Dihedral : 5.427 57.226 1272 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.09 % Allowed : 18.02 % Favored : 78.89 % 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: 1.35 (0.27), residues: 1018 helix: 2.32 (0.26), residues: 418 sheet: 0.58 (0.32), residues: 218 loop : -0.51 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.005 0.001 HIS A 127 PHE 0.027 0.001 PHE A 119 TYR 0.012 0.001 TYR B 391 ARG 0.009 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 0.878 Fit side-chains REVERT: A 92 MET cc_start: 0.6536 (tpp) cc_final: 0.6216 (mmt) REVERT: A 179 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7453 (tp) REVERT: A 185 MET cc_start: 0.7606 (tmm) cc_final: 0.7314 (tmm) REVERT: A 296 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.7768 (p) REVERT: A 300 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7739 (mtp180) REVERT: B 211 LYS cc_start: 0.8503 (mttp) cc_final: 0.7611 (mmtm) REVERT: B 218 ASN cc_start: 0.8332 (m-40) cc_final: 0.8050 (m110) REVERT: B 274 LYS cc_start: 0.7848 (tttt) cc_final: 0.7485 (ttpt) REVERT: B 280 ARG cc_start: 0.7837 (ttt-90) cc_final: 0.7538 (ttt-90) REVERT: B 317 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7311 (ptp-110) REVERT: B 318 TYR cc_start: 0.8341 (t80) cc_final: 0.8017 (t80) REVERT: B 330 GLU cc_start: 0.8054 (tt0) cc_final: 0.7785 (tt0) REVERT: C 197 ARG cc_start: 0.7111 (mtp-110) cc_final: 0.6670 (mtp85) REVERT: C 214 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.6420 (mpp80) REVERT: E 3 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6137 (tm-30) outliers start: 24 outliers final: 8 residues processed: 153 average time/residue: 1.1292 time to fit residues: 183.4527 Evaluate side-chains 138 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 0.0020 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 93 optimal weight: 0.0980 chunk 10 optimal weight: 0.1980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN B 227 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 176 GLN C 220 GLN E 31 ASN E 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8014 Z= 0.151 Angle : 0.498 7.304 10927 Z= 0.262 Chirality : 0.041 0.139 1276 Planarity : 0.004 0.060 1371 Dihedral : 5.271 56.164 1272 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.83 % Allowed : 19.05 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.27), residues: 1018 helix: 2.40 (0.26), residues: 419 sheet: 0.59 (0.32), residues: 220 loop : -0.45 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.005 0.001 HIS A 127 PHE 0.027 0.001 PHE A 119 TYR 0.011 0.001 TYR B 339 ARG 0.012 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 0.875 Fit side-chains REVERT: A 22 TYR cc_start: 0.7622 (m-80) cc_final: 0.6699 (m-80) REVERT: A 92 MET cc_start: 0.6793 (tpp) cc_final: 0.6537 (mmp) REVERT: A 145 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.6958 (mp) REVERT: A 179 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7470 (tp) REVERT: A 185 MET cc_start: 0.7615 (tmm) cc_final: 0.7396 (tmm) REVERT: A 296 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7778 (p) REVERT: A 300 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7665 (mtp180) REVERT: B 211 LYS cc_start: 0.8470 (mttp) cc_final: 0.7595 (mmtm) REVERT: B 218 ASN cc_start: 0.8372 (m-40) cc_final: 0.8163 (m110) REVERT: B 274 LYS cc_start: 0.7782 (tttt) cc_final: 0.7464 (ttpt) REVERT: B 280 ARG cc_start: 0.7779 (ttt-90) cc_final: 0.7537 (ttt-90) REVERT: B 317 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7273 (ptp-110) REVERT: B 318 TYR cc_start: 0.8315 (t80) cc_final: 0.8034 (t80) REVERT: B 330 GLU cc_start: 0.8046 (tt0) cc_final: 0.7787 (tt0) REVERT: C 197 ARG cc_start: 0.7134 (mtp-110) cc_final: 0.6680 (mtp85) REVERT: C 214 ARG cc_start: 0.6631 (mpp80) cc_final: 0.6387 (mpp80) REVERT: E 3 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6217 (tm-30) REVERT: E 80 TYR cc_start: 0.7457 (m-80) cc_final: 0.6887 (m-80) outliers start: 22 outliers final: 7 residues processed: 147 average time/residue: 1.1391 time to fit residues: 177.8083 Evaluate side-chains 135 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 3 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 0.0040 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN C 156 GLN C 175 GLN C 176 GLN C 220 GLN E 31 ASN E 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8014 Z= 0.174 Angle : 0.505 7.308 10927 Z= 0.266 Chirality : 0.041 0.135 1276 Planarity : 0.004 0.055 1371 Dihedral : 5.301 57.573 1272 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.19 % Allowed : 19.18 % Favored : 78.64 % 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: 1.46 (0.27), residues: 1018 helix: 2.39 (0.26), residues: 419 sheet: 0.60 (0.33), residues: 222 loop : -0.40 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.005 0.001 HIS B 357 PHE 0.027 0.002 PHE A 119 TYR 0.015 0.001 TYR A 246 ARG 0.007 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 0.944 Fit side-chains REVERT: A 22 TYR cc_start: 0.7742 (m-80) cc_final: 0.6776 (m-80) REVERT: A 92 MET cc_start: 0.7068 (tpp) cc_final: 0.6751 (mmp) REVERT: A 102 MET cc_start: 0.7710 (ttm) cc_final: 0.7376 (ttt) REVERT: A 145 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7002 (mp) REVERT: A 185 MET cc_start: 0.7590 (tmm) cc_final: 0.7309 (tmm) REVERT: A 296 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.7802 (p) REVERT: A 300 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7692 (mtp180) REVERT: B 211 LYS cc_start: 0.8501 (mttp) cc_final: 0.7797 (mttm) REVERT: B 274 LYS cc_start: 0.7797 (tttt) cc_final: 0.7460 (ttpt) REVERT: B 280 ARG cc_start: 0.7826 (ttt-90) cc_final: 0.7490 (ttt-90) REVERT: B 317 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7227 (ptp-110) REVERT: B 318 TYR cc_start: 0.8349 (t80) cc_final: 0.8054 (t80) REVERT: B 330 GLU cc_start: 0.8060 (tt0) cc_final: 0.7768 (tt0) REVERT: C 197 ARG cc_start: 0.7142 (mtp-110) cc_final: 0.6678 (mtp85) REVERT: C 214 ARG cc_start: 0.6631 (mpp80) cc_final: 0.6423 (mpp80) REVERT: E 3 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6223 (tm-30) REVERT: E 80 TYR cc_start: 0.7506 (m-80) cc_final: 0.7006 (m-80) outliers start: 17 outliers final: 11 residues processed: 141 average time/residue: 1.0967 time to fit residues: 164.5416 Evaluate side-chains 139 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 176 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8014 Z= 0.271 Angle : 0.575 7.204 10927 Z= 0.300 Chirality : 0.044 0.145 1276 Planarity : 0.004 0.055 1371 Dihedral : 5.708 58.910 1272 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.57 % Allowed : 19.05 % Favored : 78.38 % 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: 1.41 (0.27), residues: 1018 helix: 2.37 (0.26), residues: 412 sheet: 0.41 (0.33), residues: 221 loop : -0.30 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 118 HIS 0.009 0.001 HIS B 357 PHE 0.028 0.002 PHE A 119 TYR 0.015 0.002 TYR E 95 ARG 0.011 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.7338 (mt) cc_final: 0.7137 (mt) REVERT: A 92 MET cc_start: 0.7370 (tpp) cc_final: 0.7035 (mmp) REVERT: A 145 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7327 (mm) REVERT: A 185 MET cc_start: 0.7578 (tmm) cc_final: 0.7214 (tmm) REVERT: A 296 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.7870 (p) REVERT: A 300 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7797 (mtp180) REVERT: B 239 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8675 (p0) REVERT: B 274 LYS cc_start: 0.7725 (tttt) cc_final: 0.7384 (ttpt) REVERT: B 280 ARG cc_start: 0.7868 (ttt-90) cc_final: 0.7542 (ttt-90) REVERT: B 317 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7293 (ptp-110) REVERT: B 370 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6731 (mm-30) REVERT: C 45 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8501 (mmm) REVERT: C 137 ARG cc_start: 0.7134 (mtp-110) cc_final: 0.6876 (mtp85) outliers start: 20 outliers final: 10 residues processed: 153 average time/residue: 0.9953 time to fit residues: 162.8728 Evaluate side-chains 149 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 0.0980 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 94 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 175 GLN C 176 GLN C 220 GLN E 31 ASN E 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8014 Z= 0.161 Angle : 0.515 7.029 10927 Z= 0.271 Chirality : 0.041 0.133 1276 Planarity : 0.004 0.055 1371 Dihedral : 5.384 54.516 1272 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.80 % Allowed : 21.11 % Favored : 77.09 % 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: 1.38 (0.27), residues: 1018 helix: 2.25 (0.26), residues: 422 sheet: 0.62 (0.34), residues: 212 loop : -0.39 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.005 0.001 HIS B 220 PHE 0.027 0.001 PHE A 119 TYR 0.013 0.001 TYR B 391 ARG 0.011 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7876 (m-80) cc_final: 0.6731 (m-80) REVERT: A 38 ILE cc_start: 0.7589 (tp) cc_final: 0.7335 (mt) REVERT: A 92 MET cc_start: 0.7282 (tpp) cc_final: 0.7011 (mmp) REVERT: A 145 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.6936 (mp) REVERT: A 185 MET cc_start: 0.7606 (tmm) cc_final: 0.7277 (tmm) REVERT: A 275 SER cc_start: 0.8330 (m) cc_final: 0.7918 (m) REVERT: A 296 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.7858 (p) REVERT: B 32 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7824 (ttmt) REVERT: B 211 LYS cc_start: 0.8437 (mttp) cc_final: 0.7846 (mttm) REVERT: B 274 LYS cc_start: 0.7795 (tttt) cc_final: 0.7461 (ttpt) REVERT: B 280 ARG cc_start: 0.7834 (ttt-90) cc_final: 0.7519 (ttt-90) REVERT: B 317 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7332 (ptp-110) REVERT: B 330 GLU cc_start: 0.8102 (tt0) cc_final: 0.7750 (tt0) REVERT: B 370 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6830 (mm-30) REVERT: C 45 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8444 (mmm) REVERT: C 197 ARG cc_start: 0.7297 (ttm-80) cc_final: 0.6940 (mtp85) outliers start: 14 outliers final: 10 residues processed: 143 average time/residue: 1.0865 time to fit residues: 165.7913 Evaluate side-chains 138 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 0.0570 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 0.0470 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 0.0000 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN B 213 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 175 GLN C 176 GLN C 220 GLN E 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8014 Z= 0.160 Angle : 0.521 8.074 10927 Z= 0.272 Chirality : 0.041 0.130 1276 Planarity : 0.004 0.055 1371 Dihedral : 5.337 56.209 1272 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.67 % Allowed : 20.98 % Favored : 77.35 % 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: 1.41 (0.27), residues: 1018 helix: 2.29 (0.26), residues: 421 sheet: 0.60 (0.33), residues: 222 loop : -0.40 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.005 0.001 HIS B 220 PHE 0.026 0.001 PHE A 119 TYR 0.018 0.001 TYR A 78 ARG 0.013 0.001 ARG C 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 0.851 Fit side-chains REVERT: A 22 TYR cc_start: 0.7836 (m-80) cc_final: 0.6855 (m-80) REVERT: A 92 MET cc_start: 0.7284 (tpp) cc_final: 0.7000 (mmp) REVERT: A 185 MET cc_start: 0.7586 (tmm) cc_final: 0.7275 (tmm) REVERT: A 275 SER cc_start: 0.8338 (m) cc_final: 0.7939 (m) REVERT: A 296 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7844 (p) REVERT: B 211 LYS cc_start: 0.8441 (mttp) cc_final: 0.7836 (mttm) REVERT: B 239 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8463 (p0) REVERT: B 274 LYS cc_start: 0.7792 (tttt) cc_final: 0.7455 (ttpt) REVERT: B 280 ARG cc_start: 0.7799 (ttt-90) cc_final: 0.7481 (ttt-90) REVERT: B 317 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7381 (ptp-110) REVERT: B 330 GLU cc_start: 0.8156 (tt0) cc_final: 0.7852 (tt0) REVERT: B 370 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6870 (mm-30) REVERT: C 45 MET cc_start: 0.8737 (mtt) cc_final: 0.8443 (mmm) REVERT: C 137 ARG cc_start: 0.7007 (mtp-110) cc_final: 0.6755 (mtp85) REVERT: C 197 ARG cc_start: 0.7272 (ttm-80) cc_final: 0.6914 (mtp85) outliers start: 13 outliers final: 9 residues processed: 136 average time/residue: 1.1398 time to fit residues: 165.1031 Evaluate side-chains 138 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 0.0370 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN C 156 GLN C 175 GLN C 176 GLN C 220 GLN E 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.157706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.120856 restraints weight = 17220.312| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.97 r_work: 0.3285 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8014 Z= 0.172 Angle : 0.524 7.280 10927 Z= 0.271 Chirality : 0.042 0.131 1276 Planarity : 0.004 0.055 1371 Dihedral : 5.343 56.813 1272 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.67 % Allowed : 21.11 % Favored : 77.22 % 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: 1.40 (0.27), residues: 1018 helix: 2.28 (0.26), residues: 421 sheet: 0.61 (0.33), residues: 222 loop : -0.41 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.005 0.001 HIS B 220 PHE 0.027 0.001 PHE A 119 TYR 0.011 0.001 TYR B 339 ARG 0.013 0.000 ARG C 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3443.86 seconds wall clock time: 60 minutes 46.48 seconds (3646.48 seconds total)