Starting phenix.real_space_refine on Fri Jul 25 07:18:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k0x_61958/07_2025/9k0x_61958.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k0x_61958/07_2025/9k0x_61958.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/cci-nas-00/data/ceres_data/9k0x_61958/07_2025/9k0x_61958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k0x_61958/07_2025/9k0x_61958.map" model { file = "/net/cci-nas-00/data/ceres_data/9k0x_61958/07_2025/9k0x_61958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k0x_61958/07_2025/9k0x_61958.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= -0.001 sd= 0.152 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 3 5.49 5 S 52 5.16 5 C 4675 2.51 5 N 1259 2.21 5 O 1311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7300 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1631 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 204} Chain breaks: 3 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2339 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 5, 'TRANS': 321} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLU:plan': 3, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 122 Chain: "G" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 231 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "I" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2166 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 9, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "N" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 902 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 119} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.84, per 1000 atoms: 0.66 Number of scatterers: 7300 At special positions: 0 Unit cell: (73.5593, 96.6152, 128.454, 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 52 16.00 P 3 15.00 O 1311 8.00 N 1259 7.00 C 4675 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 278 " distance=2.03 Simple disulfide: pdb=" SG CYS I 106 " - pdb=" SG CYS I 183 " 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 11 sheets defined 40.4% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 13 through 38 removed outlier: 3.635A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.781A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.668A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.534A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.987A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 316' Processing helix chain 'A' and resid 333 through 353 removed outlier: 4.142A 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 15 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 15 through 24 removed outlier: 3.845A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.790A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'I' and resid 31 through 61 Proline residue: I 37 - end of helix Processing helix chain 'I' and resid 66 through 95 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 104 through 137 Processing helix chain 'I' and resid 139 through 143 Processing helix chain 'I' and resid 148 through 172 removed outlier: 4.222A pdb=" N ARG I 152 " --> pdb=" O ARG I 148 " (cutoff:3.500A) Proline residue: I 167 - end of helix removed outlier: 3.934A pdb=" N TYR I 170 " --> pdb=" O ALA I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 226 removed outlier: 4.516A pdb=" N VAL I 209 " --> pdb=" O LEU I 205 " (cutoff:3.500A) Proline residue: I 210 - end of helix Processing helix chain 'I' and resid 238 through 274 removed outlier: 4.491A pdb=" N VAL I 244 " --> pdb=" O LYS I 240 " (cutoff:3.500A) Proline residue: I 260 - end of helix Processing helix chain 'I' and resid 277 through 308 Proline residue: I 293 - end of helix removed outlier: 3.956A pdb=" N SER I 299 " --> pdb=" O ALA I 295 " (cutoff:3.500A) Proline residue: I 303 - end of helix Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.759A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 9.313A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.597A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.699A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.871A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.801A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.760A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.700A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.548A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 174 through 176 Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 5 removed outlier: 3.565A pdb=" N LEU N 20 " --> pdb=" O LEU N 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 50 through 51 375 hydrogen bonds defined for protein. 1080 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: 2.42 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2185 1.34 - 1.46: 1586 1.46 - 1.58: 3620 1.58 - 1.70: 5 1.70 - 1.82: 67 Bond restraints: 7463 Sorted by residual: bond pdb=" C6 ATP I 401 " pdb=" N6 ATP I 401 " ideal model delta sigma weight residual 1.337 1.415 -0.078 1.10e-02 8.26e+03 5.03e+01 bond pdb=" C5 ATP I 401 " pdb=" N7 ATP I 401 " ideal model delta sigma weight residual 1.387 1.330 0.057 1.00e-02 1.00e+04 3.27e+01 bond pdb=" C8 ATP I 401 " pdb=" N9 ATP I 401 " ideal model delta sigma weight residual 1.370 1.305 0.065 1.20e-02 6.94e+03 2.98e+01 bond pdb=" C4 ATP I 401 " pdb=" N9 ATP I 401 " ideal model delta sigma weight residual 1.374 1.327 0.047 1.00e-02 1.00e+04 2.24e+01 bond pdb=" O5' ATP I 401 " pdb=" PA ATP I 401 " ideal model delta sigma weight residual 1.579 1.627 -0.048 1.10e-02 8.26e+03 1.94e+01 ... (remaining 7458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.74: 10161 5.74 - 11.48: 20 11.48 - 17.22: 2 17.22 - 22.96: 1 22.96 - 28.70: 1 Bond angle restraints: 10185 Sorted by residual: angle pdb=" PB ATP I 401 " pdb=" O3B ATP I 401 " pdb=" PG ATP I 401 " ideal model delta sigma weight residual 139.87 111.17 28.70 1.00e+00 1.00e+00 8.24e+02 angle pdb=" PA ATP I 401 " pdb=" O3A ATP I 401 " pdb=" PB ATP I 401 " ideal model delta sigma weight residual 136.83 114.75 22.08 1.00e+00 1.00e+00 4.87e+02 angle pdb=" C5' ATP I 401 " pdb=" O5' ATP I 401 " pdb=" PA ATP I 401 " ideal model delta sigma weight residual 121.27 109.03 12.24 1.00e+00 1.00e+00 1.50e+02 angle pdb=" O3A ATP I 401 " pdb=" PB ATP I 401 " pdb=" O3B ATP I 401 " ideal model delta sigma weight residual 101.57 115.01 -13.44 1.54e+00 4.24e-01 7.66e+01 angle pdb=" N1 ATP I 401 " pdb=" C2 ATP I 401 " pdb=" N3 ATP I 401 " ideal model delta sigma weight residual 128.69 121.35 7.34 1.00e+00 1.00e+00 5.39e+01 ... (remaining 10180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3817 17.98 - 35.96: 421 35.96 - 53.93: 104 53.93 - 71.91: 20 71.91 - 89.89: 4 Dihedral angle restraints: 4366 sinusoidal: 1508 harmonic: 2858 Sorted by residual: 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 29.86 63.14 1 1.00e+01 1.00e-02 5.26e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -119.54 33.54 1 1.00e+01 1.00e-02 1.60e+01 dihedral pdb=" C LEU I 226 " pdb=" N LEU I 226 " pdb=" CA LEU I 226 " pdb=" CB LEU I 226 " ideal model delta harmonic sigma weight residual -122.60 -132.56 9.96 0 2.50e+00 1.60e-01 1.59e+01 ... (remaining 4363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1068 0.075 - 0.149: 123 0.149 - 0.224: 5 0.224 - 0.299: 1 0.299 - 0.373: 1 Chirality restraints: 1198 Sorted by residual: chirality pdb=" CA LEU I 226 " pdb=" N LEU I 226 " pdb=" C LEU I 226 " pdb=" CB LEU I 226 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CB THR I 186 " pdb=" CA THR I 186 " pdb=" OG1 THR I 186 " pdb=" CG2 THR I 186 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ARG I 143 " pdb=" N ARG I 143 " pdb=" C ARG I 143 " pdb=" CB ARG I 143 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1195 not shown) Planarity restraints: 1273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN N 13 " -0.040 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO N 14 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA N 40 " 0.035 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO N 41 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO N 41 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO N 41 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO B 236 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.028 5.00e-02 4.00e+02 ... (remaining 1270 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1240 2.76 - 3.30: 6623 3.30 - 3.83: 12508 3.83 - 4.37: 14580 4.37 - 4.90: 26014 Nonbonded interactions: 60965 Sorted by model distance: nonbonded pdb=" OG SER A 251 " pdb=" O LYS A 293 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLN N 39 " pdb=" OH TYR N 95 " model vdw 2.236 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.273 3.040 nonbonded pdb=" O GLY A 52 " pdb=" OG1 THR A 55 " model vdw 2.300 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.306 3.040 ... (remaining 60960 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: 0.610 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.650 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 7467 Z= 0.270 Angle : 0.820 28.701 10193 Z= 0.569 Chirality : 0.047 0.373 1198 Planarity : 0.005 0.061 1273 Dihedral : 16.091 89.890 2508 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 24.90 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.27), residues: 961 helix: 0.93 (0.26), residues: 370 sheet: -0.29 (0.34), residues: 235 loop : -1.58 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.007 0.001 HIS B 183 PHE 0.027 0.002 PHE I 31 TYR 0.029 0.002 TYR I 170 ARG 0.007 0.000 ARG I 140 Details of bonding type rmsd hydrogen bonds : bond 0.16443 ( 375) hydrogen bonds : angle 6.47911 ( 1080) SS BOND : bond 0.00439 ( 4) SS BOND : angle 0.87957 ( 8) covalent geometry : bond 0.00447 ( 7463) covalent geometry : angle 0.82029 (10185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.765 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 95 average time/residue: 0.8959 time to fit residues: 91.6888 Evaluate side-chains 80 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 205 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 55 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 239 ASN B 239 ASN I 130 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.204052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.165431 restraints weight = 7428.951| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.59 r_work: 0.3694 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7467 Z= 0.126 Angle : 0.502 5.569 10193 Z= 0.275 Chirality : 0.042 0.191 1198 Planarity : 0.004 0.050 1273 Dihedral : 6.594 75.272 1097 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.92 % Allowed : 22.38 % Favored : 73.71 % 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: 0.07 (0.27), residues: 961 helix: 1.53 (0.27), residues: 373 sheet: -0.11 (0.36), residues: 224 loop : -1.42 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.017 0.001 PHE I 195 TYR 0.010 0.001 TYR I 170 ARG 0.004 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04462 ( 375) hydrogen bonds : angle 4.79452 ( 1080) SS BOND : bond 0.00279 ( 4) SS BOND : angle 1.10707 ( 8) covalent geometry : bond 0.00269 ( 7463) covalent geometry : angle 0.50158 (10185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.813 Fit side-chains REVERT: B 256 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6207 (mpp80) REVERT: N 65 LYS cc_start: 0.6457 (OUTLIER) cc_final: 0.6003 (ttmt) outliers start: 28 outliers final: 15 residues processed: 114 average time/residue: 0.7913 time to fit residues: 98.0799 Evaluate side-chains 100 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain I residue 44 CYS Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 51 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 0.0870 chunk 71 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 239 ASN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.202158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.163145 restraints weight = 7599.847| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.62 r_work: 0.3663 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7467 Z= 0.144 Angle : 0.518 6.016 10193 Z= 0.280 Chirality : 0.042 0.169 1198 Planarity : 0.004 0.048 1273 Dihedral : 6.536 81.927 1095 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.17 % Allowed : 22.52 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.27), residues: 961 helix: 1.67 (0.27), residues: 375 sheet: -0.01 (0.35), residues: 223 loop : -1.47 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.018 0.002 PHE I 195 TYR 0.010 0.001 TYR B 124 ARG 0.004 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04515 ( 375) hydrogen bonds : angle 4.65705 ( 1080) SS BOND : bond 0.00296 ( 4) SS BOND : angle 1.08649 ( 8) covalent geometry : bond 0.00322 ( 7463) covalent geometry : angle 0.51705 (10185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 87 time to evaluate : 0.808 Fit side-chains REVERT: A 266 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6970 (mm) REVERT: B 118 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7628 (p0) REVERT: B 153 ASP cc_start: 0.8838 (p0) cc_final: 0.8518 (p0) REVERT: B 219 ARG cc_start: 0.8266 (mtm180) cc_final: 0.7895 (mtt-85) REVERT: B 256 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6992 (mpp80) REVERT: I 286 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6978 (mmt) outliers start: 37 outliers final: 16 residues processed: 116 average time/residue: 0.8682 time to fit residues: 108.7460 Evaluate side-chains 102 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain I residue 44 CYS Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 286 MET Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 0.0010 chunk 42 optimal weight: 0.0670 overall best weight: 0.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 239 ASN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.205634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.166618 restraints weight = 7538.092| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.62 r_work: 0.3702 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7467 Z= 0.101 Angle : 0.467 6.872 10193 Z= 0.252 Chirality : 0.041 0.150 1198 Planarity : 0.004 0.045 1273 Dihedral : 6.343 86.757 1095 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.06 % Allowed : 24.06 % Favored : 71.89 % 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: 0.42 (0.27), residues: 961 helix: 1.99 (0.27), residues: 374 sheet: 0.22 (0.37), residues: 205 loop : -1.46 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.016 0.001 PHE I 195 TYR 0.015 0.001 TYR I 170 ARG 0.002 0.000 ARG I 140 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 375) hydrogen bonds : angle 4.35565 ( 1080) SS BOND : bond 0.00093 ( 4) SS BOND : angle 1.07549 ( 8) covalent geometry : bond 0.00213 ( 7463) covalent geometry : angle 0.46583 (10185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 1.309 Fit side-chains REVERT: A 266 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6950 (mm) REVERT: A 378 ASP cc_start: 0.7244 (m-30) cc_final: 0.7003 (m-30) REVERT: B 153 ASP cc_start: 0.8705 (p0) cc_final: 0.8410 (p0) REVERT: B 219 ARG cc_start: 0.8243 (mtm180) cc_final: 0.7955 (mtt-85) REVERT: B 256 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6960 (mtp85) REVERT: N 34 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.6815 (mtp) outliers start: 29 outliers final: 14 residues processed: 111 average time/residue: 1.1672 time to fit residues: 140.1251 Evaluate side-chains 100 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain I residue 44 CYS Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 286 MET Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.202685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.163381 restraints weight = 7484.452| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.57 r_work: 0.3633 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7467 Z= 0.145 Angle : 0.522 6.334 10193 Z= 0.279 Chirality : 0.042 0.135 1198 Planarity : 0.004 0.045 1273 Dihedral : 6.528 85.513 1095 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.17 % Allowed : 22.94 % Favored : 71.89 % 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: 0.36 (0.28), residues: 961 helix: 1.91 (0.27), residues: 373 sheet: 0.12 (0.36), residues: 217 loop : -1.47 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.002 PHE I 31 TYR 0.016 0.001 TYR N 60 ARG 0.003 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 375) hydrogen bonds : angle 4.47863 ( 1080) SS BOND : bond 0.00216 ( 4) SS BOND : angle 1.22850 ( 8) covalent geometry : bond 0.00328 ( 7463) covalent geometry : angle 0.52109 (10185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 1.544 Fit side-chains REVERT: B 118 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7461 (p0) REVERT: B 153 ASP cc_start: 0.8933 (p0) cc_final: 0.8595 (p0) REVERT: B 219 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7972 (mtt-85) REVERT: B 256 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7196 (mpp80) REVERT: N 70 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.6212 (pt) outliers start: 37 outliers final: 23 residues processed: 115 average time/residue: 1.2515 time to fit residues: 156.2448 Evaluate side-chains 108 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain I residue 44 CYS Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.203262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.164946 restraints weight = 7509.718| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.58 r_work: 0.3632 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7467 Z= 0.130 Angle : 0.518 11.179 10193 Z= 0.274 Chirality : 0.042 0.142 1198 Planarity : 0.004 0.044 1273 Dihedral : 6.484 85.843 1095 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.59 % Allowed : 23.64 % Favored : 70.77 % 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: 0.42 (0.28), residues: 961 helix: 1.94 (0.27), residues: 375 sheet: 0.13 (0.36), residues: 218 loop : -1.42 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 362 PHE 0.017 0.002 PHE I 31 TYR 0.016 0.001 TYR I 170 ARG 0.003 0.000 ARG I 140 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 375) hydrogen bonds : angle 4.42621 ( 1080) SS BOND : bond 0.00223 ( 4) SS BOND : angle 1.14025 ( 8) covalent geometry : bond 0.00289 ( 7463) covalent geometry : angle 0.51765 (10185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 81 time to evaluate : 0.836 Fit side-chains REVERT: B 153 ASP cc_start: 0.8912 (p0) cc_final: 0.8623 (p0) REVERT: B 219 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7996 (mtt-85) REVERT: B 256 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7237 (mpp80) REVERT: G 25 ILE cc_start: 0.4123 (OUTLIER) cc_final: 0.3275 (pp) REVERT: N 34 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7136 (mtm) REVERT: N 70 ILE cc_start: 0.6382 (OUTLIER) cc_final: 0.6180 (pt) outliers start: 40 outliers final: 28 residues processed: 112 average time/residue: 0.8579 time to fit residues: 104.4779 Evaluate side-chains 111 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain I residue 44 CYS Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain I residue 273 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 94 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.0020 chunk 4 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.205741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.167010 restraints weight = 7524.265| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.59 r_work: 0.3667 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7467 Z= 0.104 Angle : 0.486 12.863 10193 Z= 0.256 Chirality : 0.040 0.143 1198 Planarity : 0.004 0.042 1273 Dihedral : 6.335 88.975 1095 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.34 % Allowed : 24.76 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), residues: 961 helix: 2.12 (0.28), residues: 373 sheet: 0.23 (0.36), residues: 217 loop : -1.41 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.018 0.001 PHE I 31 TYR 0.014 0.001 TYR N 60 ARG 0.006 0.000 ARG I 140 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 375) hydrogen bonds : angle 4.25262 ( 1080) SS BOND : bond 0.00211 ( 4) SS BOND : angle 1.04255 ( 8) covalent geometry : bond 0.00221 ( 7463) covalent geometry : angle 0.48569 (10185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.823 Fit side-chains REVERT: A 239 ASN cc_start: 0.7231 (t0) cc_final: 0.6569 (p0) REVERT: B 153 ASP cc_start: 0.8873 (p0) cc_final: 0.8633 (p0) REVERT: B 219 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7991 (mtt-85) REVERT: B 256 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7190 (mpp80) REVERT: G 25 ILE cc_start: 0.4111 (OUTLIER) cc_final: 0.3250 (pp) REVERT: N 34 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7067 (mtm) outliers start: 31 outliers final: 22 residues processed: 109 average time/residue: 0.8202 time to fit residues: 96.9256 Evaluate side-chains 108 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain I residue 44 CYS Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 273 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.202258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.163420 restraints weight = 7580.211| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.61 r_work: 0.3613 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7467 Z= 0.155 Angle : 0.558 15.269 10193 Z= 0.291 Chirality : 0.043 0.173 1198 Planarity : 0.004 0.043 1273 Dihedral : 6.578 86.426 1095 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.34 % Allowed : 25.31 % Favored : 70.35 % 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: 0.42 (0.28), residues: 961 helix: 1.93 (0.27), residues: 375 sheet: 0.15 (0.36), residues: 218 loop : -1.41 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.020 0.002 PHE I 31 TYR 0.017 0.002 TYR I 170 ARG 0.004 0.000 ARG I 140 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 375) hydrogen bonds : angle 4.48788 ( 1080) SS BOND : bond 0.00197 ( 4) SS BOND : angle 1.26343 ( 8) covalent geometry : bond 0.00354 ( 7463) covalent geometry : angle 0.55744 (10185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 1.043 Fit side-chains REVERT: B 118 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7462 (p0) REVERT: B 153 ASP cc_start: 0.8967 (p0) cc_final: 0.8652 (p0) REVERT: B 219 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7979 (mtt-85) REVERT: G 25 ILE cc_start: 0.4314 (OUTLIER) cc_final: 0.3421 (pp) outliers start: 31 outliers final: 23 residues processed: 106 average time/residue: 1.3811 time to fit residues: 157.3220 Evaluate side-chains 104 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain I residue 44 CYS Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 273 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 43 optimal weight: 0.0470 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.202288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.163219 restraints weight = 7611.175| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.66 r_work: 0.3633 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7467 Z= 0.147 Angle : 0.548 14.414 10193 Z= 0.287 Chirality : 0.042 0.175 1198 Planarity : 0.004 0.043 1273 Dihedral : 6.566 86.571 1095 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.20 % Allowed : 25.45 % Favored : 70.35 % 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: 0.34 (0.28), residues: 961 helix: 1.90 (0.27), residues: 373 sheet: 0.12 (0.36), residues: 218 loop : -1.50 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.021 0.002 PHE I 31 TYR 0.010 0.001 TYR I 82 ARG 0.004 0.000 ARG I 140 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 375) hydrogen bonds : angle 4.49759 ( 1080) SS BOND : bond 0.00202 ( 4) SS BOND : angle 1.26331 ( 8) covalent geometry : bond 0.00333 ( 7463) covalent geometry : angle 0.54714 (10185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.875 Fit side-chains REVERT: B 118 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7433 (p0) REVERT: B 219 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7968 (mtt-85) REVERT: G 25 ILE cc_start: 0.4208 (OUTLIER) cc_final: 0.3357 (pp) REVERT: N 70 ILE cc_start: 0.6546 (OUTLIER) cc_final: 0.6215 (tt) outliers start: 30 outliers final: 24 residues processed: 105 average time/residue: 1.2982 time to fit residues: 148.4177 Evaluate side-chains 106 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain I residue 44 CYS Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain I residue 273 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 292 ASN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.204256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.166735 restraints weight = 7580.508| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.62 r_work: 0.3672 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7467 Z= 0.116 Angle : 0.522 15.884 10193 Z= 0.272 Chirality : 0.042 0.174 1198 Planarity : 0.004 0.041 1273 Dihedral : 6.448 89.577 1095 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.64 % Allowed : 26.15 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.28), residues: 961 helix: 2.01 (0.27), residues: 373 sheet: 0.18 (0.36), residues: 218 loop : -1.45 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.023 0.001 PHE I 31 TYR 0.021 0.001 TYR I 170 ARG 0.006 0.000 ARG I 140 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 375) hydrogen bonds : angle 4.37683 ( 1080) SS BOND : bond 0.00194 ( 4) SS BOND : angle 1.13728 ( 8) covalent geometry : bond 0.00252 ( 7463) covalent geometry : angle 0.52089 (10185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.786 Fit side-chains REVERT: A 239 ASN cc_start: 0.7267 (t0) cc_final: 0.6777 (p0) REVERT: B 118 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7433 (p0) REVERT: B 153 ASP cc_start: 0.8640 (p0) cc_final: 0.8413 (p0) REVERT: B 219 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7948 (mtt-85) REVERT: G 25 ILE cc_start: 0.4194 (OUTLIER) cc_final: 0.3345 (pp) REVERT: N 70 ILE cc_start: 0.6382 (OUTLIER) cc_final: 0.6163 (tt) outliers start: 26 outliers final: 19 residues processed: 102 average time/residue: 0.7941 time to fit residues: 88.3488 Evaluate side-chains 99 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain I residue 44 CYS Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain I residue 273 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 84 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 45 optimal weight: 0.0370 chunk 91 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.204458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.165682 restraints weight = 7541.692| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.62 r_work: 0.3665 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7467 Z= 0.118 Angle : 0.523 14.389 10193 Z= 0.273 Chirality : 0.042 0.211 1198 Planarity : 0.004 0.041 1273 Dihedral : 6.320 88.143 1095 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.92 % Allowed : 25.87 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.28), residues: 961 helix: 2.04 (0.27), residues: 373 sheet: 0.14 (0.36), residues: 220 loop : -1.43 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.025 0.001 PHE I 31 TYR 0.009 0.001 TYR I 268 ARG 0.005 0.000 ARG I 140 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 375) hydrogen bonds : angle 4.34799 ( 1080) SS BOND : bond 0.00193 ( 4) SS BOND : angle 1.17619 ( 8) covalent geometry : bond 0.00259 ( 7463) covalent geometry : angle 0.52244 (10185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5563.70 seconds wall clock time: 103 minutes 53.17 seconds (6233.17 seconds total)