Starting phenix.real_space_refine on Wed Mar 12 20:37:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s8m_24897/03_2025/7s8m_24897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s8m_24897/03_2025/7s8m_24897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s8m_24897/03_2025/7s8m_24897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s8m_24897/03_2025/7s8m_24897.map" model { file = "/net/cci-nas-00/data/ceres_data/7s8m_24897/03_2025/7s8m_24897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s8m_24897/03_2025/7s8m_24897.cif" } resolution = 2.54 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5343 2.51 5 N 1408 2.21 5 O 1532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8346 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1707 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2564 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 401 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1743 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1892 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 7, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 39 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 6.25, per 1000 atoms: 0.75 Number of scatterers: 8346 At special positions: 0 Unit cell: (102.08, 117.92, 117.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1532 8.00 N 1408 7.00 C 5343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.2 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 36.9% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.667A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 281 removed outlier: 4.144A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.541A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 310 removed outlier: 3.683A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 351 removed outlier: 3.633A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 24 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.501A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.823A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 57 removed outlier: 3.966A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL R 43 " --> pdb=" O PHE R 39 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY R 44 " --> pdb=" O ILE R 40 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE R 57 " --> pdb=" O TRP R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 95 removed outlier: 3.779A pdb=" N VAL R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 133 removed outlier: 3.874A pdb=" N THR R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 167 Processing helix chain 'R' and resid 177 through 212 Processing helix chain 'R' and resid 217 through 236 Processing helix chain 'R' and resid 236 through 250 removed outlier: 4.291A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU R 247 " --> pdb=" O TRP R 243 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TRP R 248 " --> pdb=" O PHE R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 280 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 190 Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.293A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.826A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.908A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.142A 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: 3.585A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.992A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.522A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.541A 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: 3.554A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (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: 5.996A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.996A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.338A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1239 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: 2.53 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2666 1.34 - 1.46: 1967 1.46 - 1.58: 3802 1.58 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 8522 Sorted by residual: bond pdb=" CB ASP R 75 " pdb=" CG ASP R 75 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.37e+00 bond pdb=" CG1 ILE C 58 " pdb=" CD1 ILE C 58 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.22e+00 bond pdb=" CG LEU R 237 " pdb=" CD1 LEU R 237 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.02e+00 bond pdb=" C GLU E 222 " pdb=" N TYR E 223 " ideal model delta sigma weight residual 1.330 1.318 0.012 1.47e-02 4.63e+03 7.05e-01 bond pdb=" CG LEU R 45 " pdb=" CD2 LEU R 45 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.66e-01 ... (remaining 8517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 11209 1.41 - 2.81: 294 2.81 - 4.22: 48 4.22 - 5.63: 17 5.63 - 7.04: 5 Bond angle restraints: 11573 Sorted by residual: angle pdb=" N PRO E 224 " pdb=" CA PRO E 224 " pdb=" C PRO E 224 " ideal model delta sigma weight residual 112.10 118.27 -6.17 2.60e+00 1.48e-01 5.64e+00 angle pdb=" N GLY B 352 " pdb=" CA GLY B 352 " pdb=" C GLY B 352 " ideal model delta sigma weight residual 114.67 117.97 -3.30 1.41e+00 5.03e-01 5.47e+00 angle pdb=" N ASP C 291 " pdb=" CA ASP C 291 " pdb=" C ASP C 291 " ideal model delta sigma weight residual 112.97 110.60 2.37 1.06e+00 8.90e-01 5.01e+00 angle pdb=" CA TYR E 178 " pdb=" CB TYR E 178 " pdb=" CG TYR E 178 " ideal model delta sigma weight residual 113.90 117.79 -3.89 1.80e+00 3.09e-01 4.66e+00 angle pdb=" CA ARG E 206 " pdb=" CB ARG E 206 " pdb=" CG ARG E 206 " ideal model delta sigma weight residual 114.10 118.19 -4.09 2.00e+00 2.50e-01 4.19e+00 ... (remaining 11568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 4587 16.95 - 33.89: 316 33.89 - 50.84: 68 50.84 - 67.78: 11 67.78 - 84.73: 5 Dihedral angle restraints: 4987 sinusoidal: 1808 harmonic: 3179 Sorted by residual: dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual -180.00 -154.06 -25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASN B 347 " pdb=" C ASN B 347 " pdb=" N LEU B 348 " pdb=" CA LEU B 348 " ideal model delta harmonic sigma weight residual 180.00 157.57 22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 160.41 19.59 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 4984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 838 0.033 - 0.066: 344 0.066 - 0.099: 105 0.099 - 0.133: 49 0.133 - 0.166: 8 Chirality restraints: 1344 Sorted by residual: chirality pdb=" CA TYR E 178 " pdb=" N TYR E 178 " pdb=" C TYR E 178 " pdb=" CB TYR E 178 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA VAL E 37 " pdb=" N VAL E 37 " pdb=" C VAL E 37 " pdb=" CB VAL E 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA PRO E 224 " pdb=" N PRO E 224 " pdb=" C PRO E 224 " pdb=" CB PRO E 224 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 1341 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 129 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C LEU R 129 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU R 129 " -0.011 2.00e-02 2.50e+03 pdb=" N SER R 130 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN R 242 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C GLN R 242 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN R 242 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP R 243 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 123 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C VAL R 123 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL R 123 " -0.010 2.00e-02 2.50e+03 pdb=" N SER R 124 " -0.009 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 268 2.72 - 3.26: 8118 3.26 - 3.81: 13659 3.81 - 4.35: 16864 4.35 - 4.90: 29665 Nonbonded interactions: 68574 Sorted by model distance: nonbonded pdb=" OE2 GLU B 14 " pdb=" OG1 THR E 57 " model vdw 2.171 3.040 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.207 3.040 nonbonded pdb=" O CYS B 254 " pdb=" NZ LYS B 317 " model vdw 2.241 3.120 nonbonded pdb=" OD1 ASP B 272 " pdb=" N LEU B 273 " model vdw 2.249 3.120 ... (remaining 68569 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.700 Find NCS groups from input model: 0.140 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:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 0.043 8522 Z= 0.240 Angle : 0.589 7.037 11573 Z= 0.326 Chirality : 0.043 0.166 1344 Planarity : 0.004 0.031 1452 Dihedral : 12.635 84.726 2932 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.46 (0.26), residues: 1082 helix: 2.00 (0.28), residues: 369 sheet: 0.15 (0.29), residues: 276 loop : -1.08 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.004 0.001 HIS C 142 PHE 0.019 0.002 PHE B 189 TYR 0.018 0.002 TYR E 178 ARG 0.003 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: B 17 LYS cc_start: 0.7754 (mmtp) cc_final: 0.7523 (mmtp) REVERT: C 25 CYS cc_start: 0.7535 (p) cc_final: 0.7145 (p) REVERT: C 254 ASP cc_start: 0.7040 (t70) cc_final: 0.6791 (t0) REVERT: R 109 MET cc_start: 0.6736 (ttp) cc_final: 0.6462 (ttm) REVERT: R 280 PHE cc_start: 0.7849 (t80) cc_final: 0.7147 (t80) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.8903 time to fit residues: 192.4868 Evaluate side-chains 183 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 50 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN C 75 GLN C 268 ASN R 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.131561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.117080 restraints weight = 11002.279| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.62 r_work: 0.3498 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8522 Z= 0.241 Angle : 0.565 7.782 11573 Z= 0.297 Chirality : 0.043 0.152 1344 Planarity : 0.003 0.031 1452 Dihedral : 4.482 24.683 1173 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.14 % Allowed : 8.35 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.95 (0.26), residues: 1082 helix: 2.65 (0.28), residues: 373 sheet: 0.37 (0.29), residues: 275 loop : -1.05 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 243 HIS 0.003 0.001 HIS C 142 PHE 0.018 0.002 PHE B 189 TYR 0.020 0.002 TYR E 178 ARG 0.002 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: B 249 LEU cc_start: 0.8430 (tt) cc_final: 0.8230 (tt) REVERT: C 25 CYS cc_start: 0.7908 (p) cc_final: 0.7530 (p) REVERT: C 197 ARG cc_start: 0.7788 (mmt180) cc_final: 0.7545 (mmt180) REVERT: E 30 SER cc_start: 0.8242 (m) cc_final: 0.8027 (t) REVERT: R 45 LEU cc_start: 0.7580 (mm) cc_final: 0.7189 (mm) REVERT: R 280 PHE cc_start: 0.8174 (t80) cc_final: 0.7700 (t80) outliers start: 10 outliers final: 8 residues processed: 196 average time/residue: 0.9227 time to fit residues: 195.9281 Evaluate side-chains 192 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 184 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN C 268 ASN E 182 ASN R 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.130957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.116504 restraints weight = 11148.828| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.63 r_work: 0.3492 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8522 Z= 0.248 Angle : 0.546 7.029 11573 Z= 0.288 Chirality : 0.043 0.159 1344 Planarity : 0.003 0.033 1452 Dihedral : 4.412 25.030 1173 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.17 % Allowed : 11.21 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1082 helix: 2.71 (0.28), residues: 375 sheet: 0.31 (0.29), residues: 274 loop : -1.01 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.018 0.001 PHE B 189 TYR 0.020 0.002 TYR E 178 ARG 0.003 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: B 279 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8264 (mtmm) REVERT: C 25 CYS cc_start: 0.7911 (p) cc_final: 0.7500 (p) REVERT: C 197 ARG cc_start: 0.7791 (mmt180) cc_final: 0.7541 (mmt180) REVERT: C 217 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8245 (pmm) REVERT: C 258 ASP cc_start: 0.7415 (t0) cc_final: 0.7113 (t0) REVERT: R 45 LEU cc_start: 0.7610 (mm) cc_final: 0.7225 (mm) REVERT: R 280 PHE cc_start: 0.8205 (t80) cc_final: 0.7749 (t80) outliers start: 19 outliers final: 13 residues processed: 197 average time/residue: 0.8888 time to fit residues: 189.7952 Evaluate side-chains 202 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN C 268 ASN R 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.130794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.116315 restraints weight = 11021.606| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.63 r_work: 0.3486 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8522 Z= 0.252 Angle : 0.542 7.249 11573 Z= 0.285 Chirality : 0.043 0.159 1344 Planarity : 0.003 0.033 1452 Dihedral : 4.382 24.719 1173 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.97 % Allowed : 11.44 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.99 (0.26), residues: 1082 helix: 2.76 (0.27), residues: 375 sheet: 0.32 (0.30), residues: 266 loop : -1.04 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.018 0.001 PHE B 189 TYR 0.020 0.002 TYR E 178 ARG 0.003 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: B 243 MET cc_start: 0.8459 (tpt) cc_final: 0.8114 (tpp) REVERT: B 279 LYS cc_start: 0.8630 (mtmm) cc_final: 0.8269 (mtmm) REVERT: C 25 CYS cc_start: 0.7940 (p) cc_final: 0.7532 (p) REVERT: C 197 ARG cc_start: 0.7823 (mmt180) cc_final: 0.7535 (mmt180) REVERT: C 217 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8271 (pmm) REVERT: R 45 LEU cc_start: 0.7592 (mm) cc_final: 0.7180 (mm) REVERT: R 280 PHE cc_start: 0.8212 (t80) cc_final: 0.7729 (t80) outliers start: 26 outliers final: 15 residues processed: 201 average time/residue: 0.8398 time to fit residues: 183.4713 Evaluate side-chains 199 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 chunk 106 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS C 268 ASN E 130 GLN R 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.131403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.117076 restraints weight = 11070.455| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.62 r_work: 0.3501 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8522 Z= 0.216 Angle : 0.530 6.377 11573 Z= 0.279 Chirality : 0.042 0.153 1344 Planarity : 0.003 0.033 1452 Dihedral : 4.304 23.628 1173 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.75 % Allowed : 13.62 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.02 (0.26), residues: 1082 helix: 2.79 (0.27), residues: 375 sheet: 0.33 (0.30), residues: 266 loop : -1.01 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.017 0.001 PHE B 189 TYR 0.019 0.002 TYR E 178 ARG 0.002 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: B 243 MET cc_start: 0.8451 (tpt) cc_final: 0.8150 (tpp) REVERT: B 279 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8263 (mtmm) REVERT: C 25 CYS cc_start: 0.7911 (p) cc_final: 0.7503 (p) REVERT: C 146 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8466 (mt) REVERT: C 197 ARG cc_start: 0.7783 (mmt180) cc_final: 0.7526 (mmt180) REVERT: C 217 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8241 (pmm) REVERT: R 45 LEU cc_start: 0.7613 (mm) cc_final: 0.7244 (mm) REVERT: R 280 PHE cc_start: 0.8212 (t80) cc_final: 0.7701 (t80) outliers start: 24 outliers final: 18 residues processed: 194 average time/residue: 0.8882 time to fit residues: 186.4779 Evaluate side-chains 198 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 17 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS C 220 GLN C 268 ASN R 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.130315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.115913 restraints weight = 11045.620| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.61 r_work: 0.3482 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8522 Z= 0.298 Angle : 0.564 7.176 11573 Z= 0.297 Chirality : 0.044 0.164 1344 Planarity : 0.003 0.033 1452 Dihedral : 4.430 24.508 1173 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.97 % Allowed : 13.73 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.03 (0.26), residues: 1082 helix: 2.81 (0.27), residues: 373 sheet: 0.37 (0.30), residues: 268 loop : -1.02 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.018 0.002 PHE B 189 TYR 0.022 0.002 TYR E 178 ARG 0.003 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: B 229 ASP cc_start: 0.7163 (p0) cc_final: 0.6931 (p0) REVERT: B 243 MET cc_start: 0.8424 (tpt) cc_final: 0.8087 (tpp) REVERT: C 25 CYS cc_start: 0.7911 (p) cc_final: 0.7498 (p) REVERT: C 197 ARG cc_start: 0.7818 (mmt180) cc_final: 0.7573 (mmt180) REVERT: C 217 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8284 (pmm) REVERT: R 45 LEU cc_start: 0.7640 (mm) cc_final: 0.7263 (mm) REVERT: R 280 PHE cc_start: 0.8231 (t80) cc_final: 0.7714 (t80) outliers start: 26 outliers final: 21 residues processed: 195 average time/residue: 0.8807 time to fit residues: 186.0722 Evaluate side-chains 203 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 0 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 40 optimal weight: 0.0670 chunk 87 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS C 220 GLN C 268 ASN R 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.131198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.116760 restraints weight = 11034.143| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.63 r_work: 0.3495 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8522 Z= 0.229 Angle : 0.545 9.609 11573 Z= 0.285 Chirality : 0.043 0.156 1344 Planarity : 0.003 0.032 1452 Dihedral : 4.341 23.237 1173 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.09 % Allowed : 14.19 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.07 (0.26), residues: 1082 helix: 2.84 (0.27), residues: 373 sheet: 0.35 (0.30), residues: 268 loop : -0.98 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.017 0.001 PHE B 189 TYR 0.019 0.002 TYR E 178 ARG 0.002 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: B 243 MET cc_start: 0.8400 (tpt) cc_final: 0.8149 (tpp) REVERT: C 25 CYS cc_start: 0.7917 (p) cc_final: 0.7518 (p) REVERT: C 197 ARG cc_start: 0.7810 (mmt180) cc_final: 0.7571 (mmt180) REVERT: E 167 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: R 45 LEU cc_start: 0.7599 (mm) cc_final: 0.7242 (mm) outliers start: 27 outliers final: 24 residues processed: 196 average time/residue: 0.9345 time to fit residues: 198.5106 Evaluate side-chains 202 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 24 optimal weight: 0.0370 chunk 87 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 77 optimal weight: 0.0000 chunk 75 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS C 268 ASN R 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.131336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.116787 restraints weight = 11182.809| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.66 r_work: 0.3498 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8522 Z= 0.209 Angle : 0.551 11.556 11573 Z= 0.283 Chirality : 0.042 0.150 1344 Planarity : 0.003 0.032 1452 Dihedral : 4.267 22.126 1173 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.09 % Allowed : 14.65 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.09 (0.26), residues: 1082 helix: 2.96 (0.27), residues: 368 sheet: 0.28 (0.31), residues: 267 loop : -0.96 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.018 0.001 PHE R 280 TYR 0.018 0.001 TYR E 178 ARG 0.002 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: B 243 MET cc_start: 0.8369 (tpt) cc_final: 0.8132 (tpp) REVERT: C 25 CYS cc_start: 0.7948 (p) cc_final: 0.7532 (p) REVERT: C 197 ARG cc_start: 0.7840 (mmt180) cc_final: 0.7588 (mmt180) REVERT: E 167 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8511 (tt0) REVERT: R 45 LEU cc_start: 0.7618 (mm) cc_final: 0.7286 (mm) REVERT: R 280 PHE cc_start: 0.8133 (t80) cc_final: 0.7832 (t80) outliers start: 27 outliers final: 21 residues processed: 192 average time/residue: 0.9076 time to fit residues: 188.7050 Evaluate side-chains 197 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 84 optimal weight: 0.0980 chunk 99 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS C 268 ASN R 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.131254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.116756 restraints weight = 11076.442| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.63 r_work: 0.3496 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8522 Z= 0.239 Angle : 0.566 11.775 11573 Z= 0.290 Chirality : 0.043 0.154 1344 Planarity : 0.003 0.031 1452 Dihedral : 4.308 22.743 1173 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.52 % Allowed : 15.45 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1082 helix: 2.96 (0.27), residues: 367 sheet: 0.32 (0.31), residues: 269 loop : -0.93 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.019 0.002 PHE R 280 TYR 0.020 0.002 TYR E 178 ARG 0.002 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: B 243 MET cc_start: 0.8381 (tpt) cc_final: 0.8170 (tpp) REVERT: C 25 CYS cc_start: 0.7903 (p) cc_final: 0.7497 (p) REVERT: C 197 ARG cc_start: 0.7807 (mmt180) cc_final: 0.7567 (mmt180) REVERT: E 167 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: R 45 LEU cc_start: 0.7617 (mm) cc_final: 0.7289 (mm) REVERT: R 280 PHE cc_start: 0.8145 (t80) cc_final: 0.7813 (t80) outliers start: 22 outliers final: 20 residues processed: 187 average time/residue: 1.0290 time to fit residues: 208.4434 Evaluate side-chains 196 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS C 220 GLN C 268 ASN R 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.130702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.116185 restraints weight = 11003.910| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.62 r_work: 0.3488 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8522 Z= 0.283 Angle : 0.573 11.197 11573 Z= 0.297 Chirality : 0.043 0.160 1344 Planarity : 0.003 0.032 1452 Dihedral : 4.391 23.555 1173 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.52 % Allowed : 15.56 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.06 (0.26), residues: 1082 helix: 2.85 (0.27), residues: 373 sheet: 0.28 (0.30), residues: 274 loop : -0.96 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.019 0.002 PHE R 280 TYR 0.021 0.002 TYR E 178 ARG 0.003 0.000 ARG R 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: B 229 ASP cc_start: 0.7106 (p0) cc_final: 0.6885 (p0) REVERT: B 243 MET cc_start: 0.8402 (tpt) cc_final: 0.8152 (tpp) REVERT: C 25 CYS cc_start: 0.7897 (p) cc_final: 0.7490 (p) REVERT: C 197 ARG cc_start: 0.7818 (mmt180) cc_final: 0.7564 (mmt180) REVERT: E 167 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8520 (tt0) REVERT: R 45 LEU cc_start: 0.7631 (mm) cc_final: 0.7294 (mm) REVERT: R 280 PHE cc_start: 0.8156 (t80) cc_final: 0.7849 (t80) outliers start: 22 outliers final: 19 residues processed: 190 average time/residue: 0.9365 time to fit residues: 192.3984 Evaluate side-chains 196 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 39 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS C 220 GLN C 268 ASN R 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.130890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.116031 restraints weight = 11139.778| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.67 r_work: 0.3500 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8522 Z= 0.290 Angle : 0.580 10.912 11573 Z= 0.300 Chirality : 0.044 0.163 1344 Planarity : 0.003 0.032 1452 Dihedral : 4.423 23.593 1173 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.63 % Allowed : 15.33 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 1082 helix: 2.95 (0.27), residues: 367 sheet: 0.34 (0.31), residues: 268 loop : -0.97 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.020 0.002 PHE R 280 TYR 0.021 0.002 TYR E 178 ARG 0.003 0.000 ARG R 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7048.88 seconds wall clock time: 122 minutes 49.58 seconds (7369.58 seconds total)