Starting phenix.real_space_refine on Sun May 11 18:10:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z3m_39747/05_2025/8z3m_39747.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z3m_39747/05_2025/8z3m_39747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z3m_39747/05_2025/8z3m_39747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z3m_39747/05_2025/8z3m_39747.map" model { file = "/net/cci-nas-00/data/ceres_data/8z3m_39747/05_2025/8z3m_39747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z3m_39747/05_2025/8z3m_39747.cif" } resolution = 2.9 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= 0.002 sd= 0.032 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 46 5.16 5 C 5379 2.51 5 N 1433 2.21 5 O 1537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8395 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1783 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 118 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2458 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 10, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 96 Chain: "G" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 334 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "S" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1662 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 4, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "R" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2158 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 279} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 145 Time building chain proxies: 5.53, per 1000 atoms: 0.66 Number of scatterers: 8395 At special positions: 0 Unit cell: (94.3, 119.72, 127.1, 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 46 16.00 O 1537 8.00 N 1433 7.00 C 5379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 38.3% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.586A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.866A pdb=" N ASN A 214 " --> pdb=" O GLN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.814A pdb=" N ALA A 281 " --> pdb=" O PRO A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 317 removed outlier: 3.556A pdb=" N GLU A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 4.088A 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 'S' and resid 53 through 56 removed outlier: 4.107A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'R' and resid 18 through 48 removed outlier: 3.553A pdb=" N SER R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 50 through 79 removed outlier: 4.095A pdb=" N VAL R 54 " --> pdb=" O ASN R 50 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 94 Processing helix chain 'R' and resid 94 through 120 removed outlier: 4.414A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 129 Processing helix chain 'R' and resid 130 through 149 removed outlier: 3.568A pdb=" N ASN R 149 " --> pdb=" O GLU R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 155 removed outlier: 3.677A pdb=" N PHE R 154 " --> pdb=" O SER R 150 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS R 155 " --> pdb=" O ALA R 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 150 through 155' Processing helix chain 'R' and resid 175 through 188 Processing helix chain 'R' and resid 190 through 210 Processing helix chain 'R' and resid 215 through 254 Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 258 through 275 removed outlier: 3.715A pdb=" N GLU R 262 " --> pdb=" O CYS R 258 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N SER R 266 " --> pdb=" O GLU R 262 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ALA R 267 " --> pdb=" O ARG R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 288 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 300 removed outlier: 3.623A pdb=" N ARG R 294 " --> pdb=" O ASN R 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 182 through 189 removed outlier: 6.740A pdb=" N LEU A 34 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N PHE A 197 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU A 36 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LEU A 38 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG A 35 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 37 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL A 222 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 39 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE A 219 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N PHE A 255 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE A 221 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASN A 257 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL A 223 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.581A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.835A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.012A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.535A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.880A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.571A 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: 3.635A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.754A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.696A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 4.205A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1245 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: 2.52 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1348 1.29 - 1.42: 2372 1.42 - 1.55: 4808 1.55 - 1.69: 0 1.69 - 1.82: 64 Bond restraints: 8592 Sorted by residual: bond pdb=" C PHE R 159 " pdb=" O PHE R 159 " ideal model delta sigma weight residual 1.236 1.157 0.079 1.14e-02 7.69e+03 4.76e+01 bond pdb=" CA ALA R 249 " pdb=" C ALA R 249 " ideal model delta sigma weight residual 1.524 1.442 0.081 1.26e-02 6.30e+03 4.18e+01 bond pdb=" CA TRP R 83 " pdb=" C TRP R 83 " ideal model delta sigma weight residual 1.524 1.444 0.079 1.30e-02 5.92e+03 3.71e+01 bond pdb=" N ILE R 84 " pdb=" CA ILE R 84 " ideal model delta sigma weight residual 1.459 1.389 0.070 1.25e-02 6.40e+03 3.10e+01 bond pdb=" CA TYR R 251 " pdb=" C TYR R 251 " ideal model delta sigma weight residual 1.523 1.451 0.072 1.30e-02 5.92e+03 3.06e+01 ... (remaining 8587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 11602 2.70 - 5.40: 123 5.40 - 8.09: 9 8.09 - 10.79: 4 10.79 - 13.49: 3 Bond angle restraints: 11741 Sorted by residual: angle pdb=" N ASN R 164 " pdb=" CA ASN R 164 " pdb=" C ASN R 164 " ideal model delta sigma weight residual 112.47 124.79 -12.32 1.24e+00 6.50e-01 9.88e+01 angle pdb=" N HIS R 79 " pdb=" CA HIS R 79 " pdb=" C HIS R 79 " ideal model delta sigma weight residual 110.59 99.39 11.20 1.45e+00 4.76e-01 5.97e+01 angle pdb=" N TYR R 163 " pdb=" CA TYR R 163 " pdb=" C TYR R 163 " ideal model delta sigma weight residual 110.68 120.36 -9.68 1.39e+00 5.18e-01 4.85e+01 angle pdb=" N ILE R 84 " pdb=" CA ILE R 84 " pdb=" C ILE R 84 " ideal model delta sigma weight residual 109.34 95.85 13.49 2.08e+00 2.31e-01 4.20e+01 angle pdb=" N LYS A 270 " pdb=" CA LYS A 270 " pdb=" C LYS A 270 " ideal model delta sigma weight residual 113.40 122.74 -9.34 1.47e+00 4.63e-01 4.04e+01 ... (remaining 11736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 4464 15.20 - 30.41: 403 30.41 - 45.61: 90 45.61 - 60.82: 12 60.82 - 76.02: 8 Dihedral angle restraints: 4977 sinusoidal: 1644 harmonic: 3333 Sorted by residual: dihedral pdb=" N LYS A 270 " pdb=" C LYS A 270 " pdb=" CA LYS A 270 " pdb=" CB LYS A 270 " ideal model delta harmonic sigma weight residual 122.80 138.69 -15.89 0 2.50e+00 1.60e-01 4.04e+01 dihedral pdb=" C LYS A 270 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " pdb=" CB LYS A 270 " ideal model delta harmonic sigma weight residual -122.60 -137.84 15.24 0 2.50e+00 1.60e-01 3.72e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 131.33 -38.33 1 1.00e+01 1.00e-02 2.07e+01 ... (remaining 4974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1351 0.151 - 0.302: 12 0.302 - 0.453: 1 0.453 - 0.603: 2 0.603 - 0.754: 1 Chirality restraints: 1367 Sorted by residual: chirality pdb=" CA LYS A 270 " pdb=" N LYS A 270 " pdb=" C LYS A 270 " pdb=" CB LYS A 270 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA TYR R 163 " pdb=" N TYR R 163 " pdb=" C TYR R 163 " pdb=" CB TYR R 163 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" CA ASN R 164 " pdb=" N ASN R 164 " pdb=" C ASN R 164 " pdb=" CB ASN R 164 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.24e+00 ... (remaining 1364 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 78 " 0.013 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C LEU R 78 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU R 78 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS R 79 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET R 181 " -0.012 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C MET R 181 " 0.044 2.00e-02 2.50e+03 pdb=" O MET R 181 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN R 182 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL S 64 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.87e+00 pdb=" C VAL S 64 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL S 64 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS S 65 " -0.014 2.00e-02 2.50e+03 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 33 2.47 - 3.08: 5810 3.08 - 3.69: 13056 3.69 - 4.29: 18809 4.29 - 4.90: 31468 Nonbonded interactions: 69176 Sorted by model distance: nonbonded pdb=" O ALA A 263 " pdb=" CD1 LEU A 267 " model vdw 1.867 3.460 nonbonded pdb=" O ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.229 3.040 nonbonded pdb=" O LEU R 272 " pdb=" OG1 THR R 275 " model vdw 2.234 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.281 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.286 3.040 ... (remaining 69171 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: 0.870 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 22.510 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 0.006 0.081 8594 Z= 0.374 Angle : 0.722 13.488 11745 Z= 0.443 Chirality : 0.056 0.754 1367 Planarity : 0.004 0.050 1496 Dihedral : 12.812 76.019 2823 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.12 % Allowed : 1.12 % Favored : 98.75 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.41 % 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: 0.49 (0.26), residues: 1133 helix: 1.67 (0.27), residues: 392 sheet: 0.31 (0.30), residues: 269 loop : -0.78 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 332 HIS 0.007 0.001 HIS R 165 PHE 0.032 0.002 PHE S 68 TYR 0.016 0.001 TYR R 163 ARG 0.005 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.13649 ( 442) hydrogen bonds : angle 5.92383 ( 1245) SS BOND : bond 0.00377 ( 2) SS BOND : angle 1.00131 ( 4) covalent geometry : bond 0.00554 ( 8592) covalent geometry : angle 0.72159 (11741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 227 ASP cc_start: 0.7706 (t0) cc_final: 0.7403 (t0) REVERT: A 307 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7871 (tmm-80) REVERT: B 88 ASN cc_start: 0.7549 (m110) cc_final: 0.7313 (m110) REVERT: B 100 VAL cc_start: 0.8389 (p) cc_final: 0.8154 (m) REVERT: B 175 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7586 (mm-40) REVERT: B 178 THR cc_start: 0.8654 (m) cc_final: 0.8451 (t) REVERT: B 283 ARG cc_start: 0.8551 (tpt-90) cc_final: 0.8319 (tpp-160) REVERT: B 289 TYR cc_start: 0.8305 (m-80) cc_final: 0.7413 (m-80) REVERT: B 291 ASP cc_start: 0.6365 (t70) cc_final: 0.6161 (t0) REVERT: S 34 MET cc_start: 0.8099 (mmm) cc_final: 0.7722 (mmm) REVERT: S 128 MET cc_start: 0.8529 (mtm) cc_final: 0.8255 (mtt) REVERT: S 218 MET cc_start: 0.7909 (mtp) cc_final: 0.7574 (ttm) REVERT: R 24 TYR cc_start: 0.7973 (m-10) cc_final: 0.7705 (m-10) REVERT: R 230 ILE cc_start: 0.8289 (mm) cc_final: 0.8067 (mt) outliers start: 1 outliers final: 1 residues processed: 208 average time/residue: 0.8622 time to fit residues: 194.3612 Evaluate side-chains 192 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 110 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109707 restraints weight = 12658.875| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.91 r_work: 0.3366 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8594 Z= 0.156 Angle : 0.560 6.317 11745 Z= 0.296 Chirality : 0.043 0.144 1367 Planarity : 0.004 0.054 1496 Dihedral : 4.313 23.996 1229 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.49 % Allowed : 11.33 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.65 (0.25), residues: 1133 helix: 1.91 (0.26), residues: 392 sheet: 0.27 (0.30), residues: 261 loop : -0.69 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 83 HIS 0.005 0.001 HIS R 165 PHE 0.022 0.002 PHE S 68 TYR 0.019 0.001 TYR S 178 ARG 0.008 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 442) hydrogen bonds : angle 4.84191 ( 1245) SS BOND : bond 0.00434 ( 2) SS BOND : angle 1.27475 ( 4) covalent geometry : bond 0.00355 ( 8592) covalent geometry : angle 0.56001 (11741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.952 Fit side-chains REVERT: A 227 ASP cc_start: 0.7892 (t0) cc_final: 0.7561 (t0) REVERT: B 68 ARG cc_start: 0.8164 (tpt-90) cc_final: 0.7940 (tpt90) REVERT: B 83 ASP cc_start: 0.8237 (t0) cc_final: 0.7841 (t0) REVERT: B 155 ASN cc_start: 0.8221 (t0) cc_final: 0.7955 (t0) REVERT: B 158 VAL cc_start: 0.8401 (p) cc_final: 0.8194 (t) REVERT: B 175 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7975 (mm-40) REVERT: B 285 LEU cc_start: 0.8260 (tt) cc_final: 0.7962 (tp) REVERT: B 289 TYR cc_start: 0.8318 (m-80) cc_final: 0.7346 (m-80) REVERT: B 291 ASP cc_start: 0.6628 (t70) cc_final: 0.6403 (t0) REVERT: S 34 MET cc_start: 0.8250 (mmm) cc_final: 0.7926 (mmm) REVERT: S 143 VAL cc_start: 0.8658 (p) cc_final: 0.8339 (m) REVERT: S 180 MET cc_start: 0.8011 (ttp) cc_final: 0.7777 (ttp) REVERT: R 66 TYR cc_start: 0.8321 (t80) cc_final: 0.7923 (t80) REVERT: R 70 LEU cc_start: 0.8733 (tp) cc_final: 0.8523 (tm) REVERT: R 125 PHE cc_start: 0.8655 (m-80) cc_final: 0.8296 (m-80) REVERT: R 251 TYR cc_start: 0.8515 (t80) cc_final: 0.7896 (t80) outliers start: 20 outliers final: 10 residues processed: 214 average time/residue: 0.8535 time to fit residues: 198.4698 Evaluate side-chains 207 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 227 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 0.0000 chunk 13 optimal weight: 0.0980 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 0.0570 chunk 109 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 overall best weight: 0.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 352 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.125823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.111675 restraints weight = 12808.476| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.82 r_work: 0.3397 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8594 Z= 0.111 Angle : 0.514 6.213 11745 Z= 0.272 Chirality : 0.041 0.137 1367 Planarity : 0.004 0.051 1496 Dihedral : 3.998 24.280 1227 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.86 % Allowed : 14.32 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.77 (0.25), residues: 1133 helix: 2.14 (0.26), residues: 391 sheet: 0.14 (0.30), residues: 266 loop : -0.62 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 83 HIS 0.006 0.001 HIS R 165 PHE 0.024 0.001 PHE R 274 TYR 0.014 0.001 TYR S 178 ARG 0.009 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 442) hydrogen bonds : angle 4.54971 ( 1245) SS BOND : bond 0.00396 ( 2) SS BOND : angle 0.86803 ( 4) covalent geometry : bond 0.00247 ( 8592) covalent geometry : angle 0.51367 (11741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 227 ASP cc_start: 0.7823 (t0) cc_final: 0.7578 (t0) REVERT: B 155 ASN cc_start: 0.8129 (t0) cc_final: 0.7917 (t0) REVERT: B 175 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7915 (mm-40) REVERT: B 251 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7647 (mtm-85) REVERT: B 285 LEU cc_start: 0.8218 (tt) cc_final: 0.7951 (tp) REVERT: B 291 ASP cc_start: 0.6508 (t70) cc_final: 0.6226 (t70) REVERT: S 34 MET cc_start: 0.8177 (mmm) cc_final: 0.7814 (mmm) REVERT: S 143 VAL cc_start: 0.8689 (p) cc_final: 0.8382 (m) REVERT: S 216 TYR cc_start: 0.8054 (m-80) cc_final: 0.7849 (m-80) REVERT: S 218 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8069 (ttp) REVERT: R 124 ARG cc_start: 0.8426 (mtp180) cc_final: 0.8186 (mtp180) REVERT: R 125 PHE cc_start: 0.8621 (m-80) cc_final: 0.8242 (m-80) REVERT: R 163 TYR cc_start: 0.8291 (m-10) cc_final: 0.8010 (m-10) REVERT: R 251 TYR cc_start: 0.8441 (t80) cc_final: 0.7821 (t80) outliers start: 23 outliers final: 11 residues processed: 216 average time/residue: 0.8930 time to fit residues: 208.5302 Evaluate side-chains 215 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.110027 restraints weight = 12698.432| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.90 r_work: 0.3363 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8594 Z= 0.133 Angle : 0.521 6.105 11745 Z= 0.276 Chirality : 0.042 0.134 1367 Planarity : 0.004 0.051 1496 Dihedral : 3.980 24.141 1227 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.24 % Allowed : 16.56 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.72 (0.25), residues: 1133 helix: 2.14 (0.26), residues: 394 sheet: 0.01 (0.30), residues: 270 loop : -0.65 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS R 165 PHE 0.022 0.002 PHE S 68 TYR 0.014 0.001 TYR S 178 ARG 0.009 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 442) hydrogen bonds : angle 4.51832 ( 1245) SS BOND : bond 0.00435 ( 2) SS BOND : angle 0.93117 ( 4) covalent geometry : bond 0.00302 ( 8592) covalent geometry : angle 0.52062 (11741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.938 Fit side-chains REVERT: A 227 ASP cc_start: 0.7828 (t0) cc_final: 0.7570 (t0) REVERT: A 257 ASN cc_start: 0.8253 (t0) cc_final: 0.7969 (t0) REVERT: B 155 ASN cc_start: 0.8172 (t0) cc_final: 0.7958 (t0) REVERT: B 251 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7740 (mtm-85) REVERT: B 285 LEU cc_start: 0.8222 (tt) cc_final: 0.7967 (tp) REVERT: B 291 ASP cc_start: 0.6628 (t70) cc_final: 0.6291 (t70) REVERT: S 34 MET cc_start: 0.8256 (mmm) cc_final: 0.7902 (mmm) REVERT: S 83 MET cc_start: 0.6844 (mmm) cc_final: 0.6431 (mmm) REVERT: S 128 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8302 (mtt) REVERT: S 143 VAL cc_start: 0.8663 (p) cc_final: 0.8368 (m) REVERT: S 163 TYR cc_start: 0.8126 (m-80) cc_final: 0.7897 (m-80) REVERT: R 125 PHE cc_start: 0.8669 (m-80) cc_final: 0.8267 (m-80) REVERT: R 251 TYR cc_start: 0.8422 (t80) cc_final: 0.7798 (t80) outliers start: 26 outliers final: 15 residues processed: 200 average time/residue: 0.8765 time to fit residues: 189.9350 Evaluate side-chains 211 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 0.0970 chunk 68 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN B 225 HIS R 121 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109725 restraints weight = 12577.723| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.90 r_work: 0.3355 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8594 Z= 0.140 Angle : 0.524 6.092 11745 Z= 0.277 Chirality : 0.042 0.132 1367 Planarity : 0.004 0.052 1496 Dihedral : 3.982 24.060 1227 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.74 % Allowed : 17.81 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.74 (0.25), residues: 1133 helix: 2.14 (0.26), residues: 395 sheet: -0.00 (0.30), residues: 270 loop : -0.61 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS R 165 PHE 0.018 0.001 PHE S 68 TYR 0.014 0.001 TYR S 178 ARG 0.010 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 442) hydrogen bonds : angle 4.43496 ( 1245) SS BOND : bond 0.00404 ( 2) SS BOND : angle 0.96111 ( 4) covalent geometry : bond 0.00320 ( 8592) covalent geometry : angle 0.52384 (11741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 227 ASP cc_start: 0.7874 (t0) cc_final: 0.7651 (t0) REVERT: B 155 ASN cc_start: 0.8192 (t0) cc_final: 0.7979 (t0) REVERT: B 175 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7975 (mm-40) REVERT: B 225 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7786 (m-70) REVERT: B 251 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7841 (mtm-85) REVERT: B 285 LEU cc_start: 0.8232 (tt) cc_final: 0.7988 (tp) REVERT: B 291 ASP cc_start: 0.6690 (t70) cc_final: 0.6339 (t70) REVERT: S 34 MET cc_start: 0.8238 (mmm) cc_final: 0.7913 (mmm) REVERT: S 83 MET cc_start: 0.6934 (mmm) cc_final: 0.6569 (mmm) REVERT: S 128 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8307 (mtt) REVERT: S 143 VAL cc_start: 0.8676 (p) cc_final: 0.8391 (m) REVERT: S 160 THR cc_start: 0.8583 (p) cc_final: 0.8376 (p) REVERT: S 163 TYR cc_start: 0.8132 (m-80) cc_final: 0.7907 (m-80) REVERT: R 125 PHE cc_start: 0.8674 (m-80) cc_final: 0.8265 (m-80) outliers start: 30 outliers final: 14 residues processed: 203 average time/residue: 0.8792 time to fit residues: 193.4320 Evaluate side-chains 208 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 0.0170 overall best weight: 0.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 176 GLN B 220 GLN R 121 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.124342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110143 restraints weight = 12680.604| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.92 r_work: 0.3362 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8594 Z= 0.128 Angle : 0.529 6.576 11745 Z= 0.278 Chirality : 0.042 0.141 1367 Planarity : 0.004 0.051 1496 Dihedral : 3.939 24.156 1227 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.74 % Allowed : 19.93 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.82 (0.25), residues: 1133 helix: 2.19 (0.26), residues: 395 sheet: 0.06 (0.30), residues: 268 loop : -0.57 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.006 0.001 HIS R 165 PHE 0.016 0.001 PHE A 328 TYR 0.016 0.001 TYR S 216 ARG 0.010 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 442) hydrogen bonds : angle 4.41098 ( 1245) SS BOND : bond 0.00443 ( 2) SS BOND : angle 0.89178 ( 4) covalent geometry : bond 0.00290 ( 8592) covalent geometry : angle 0.52887 (11741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 227 ASP cc_start: 0.7876 (t0) cc_final: 0.7655 (t0) REVERT: B 155 ASN cc_start: 0.8207 (t0) cc_final: 0.7985 (t0) REVERT: B 175 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7997 (mm-40) REVERT: B 285 LEU cc_start: 0.8233 (tt) cc_final: 0.7994 (tp) REVERT: B 291 ASP cc_start: 0.6692 (t70) cc_final: 0.6321 (t70) REVERT: S 34 MET cc_start: 0.8227 (mmm) cc_final: 0.7919 (mmm) REVERT: S 83 MET cc_start: 0.7027 (mmm) cc_final: 0.6671 (mmm) REVERT: S 128 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8297 (mtt) REVERT: S 143 VAL cc_start: 0.8671 (p) cc_final: 0.8386 (m) REVERT: S 162 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7526 (tt) REVERT: S 163 TYR cc_start: 0.8148 (m-80) cc_final: 0.7763 (m-80) REVERT: R 125 PHE cc_start: 0.8677 (m-80) cc_final: 0.8281 (m-80) REVERT: R 251 TYR cc_start: 0.8419 (t80) cc_final: 0.7861 (t80) outliers start: 22 outliers final: 15 residues processed: 202 average time/residue: 0.8759 time to fit residues: 191.9490 Evaluate side-chains 211 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 106 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 85 optimal weight: 0.0980 chunk 49 optimal weight: 0.0070 chunk 31 optimal weight: 0.0170 chunk 24 optimal weight: 6.9990 overall best weight: 0.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN B 176 GLN B 225 HIS R 121 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.126596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112405 restraints weight = 12888.240| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.95 r_work: 0.3404 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8594 Z= 0.099 Angle : 0.515 6.591 11745 Z= 0.271 Chirality : 0.041 0.146 1367 Planarity : 0.004 0.049 1496 Dihedral : 3.769 23.904 1227 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.36 % Allowed : 19.93 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.94 (0.26), residues: 1133 helix: 2.39 (0.26), residues: 394 sheet: 0.06 (0.30), residues: 266 loop : -0.53 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS R 165 PHE 0.012 0.001 PHE S 68 TYR 0.018 0.001 TYR S 216 ARG 0.009 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03074 ( 442) hydrogen bonds : angle 4.25416 ( 1245) SS BOND : bond 0.00441 ( 2) SS BOND : angle 0.74868 ( 4) covalent geometry : bond 0.00207 ( 8592) covalent geometry : angle 0.51453 (11741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 227 ASP cc_start: 0.7864 (t0) cc_final: 0.7645 (t0) REVERT: A 300 THR cc_start: 0.8141 (t) cc_final: 0.7938 (m) REVERT: B 155 ASN cc_start: 0.8107 (t0) cc_final: 0.7888 (t0) REVERT: B 175 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7948 (mm-40) REVERT: B 285 LEU cc_start: 0.8204 (tt) cc_final: 0.7942 (tp) REVERT: S 34 MET cc_start: 0.8136 (mmm) cc_final: 0.7807 (mmm) REVERT: S 83 MET cc_start: 0.6922 (mmm) cc_final: 0.6677 (mmm) REVERT: S 128 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8244 (mtt) REVERT: S 143 VAL cc_start: 0.8645 (p) cc_final: 0.8353 (m) REVERT: S 163 TYR cc_start: 0.8145 (m-80) cc_final: 0.7908 (m-80) REVERT: R 125 PHE cc_start: 0.8634 (m-80) cc_final: 0.8297 (m-80) REVERT: R 251 TYR cc_start: 0.8323 (t80) cc_final: 0.7680 (t80) outliers start: 27 outliers final: 12 residues processed: 200 average time/residue: 0.8456 time to fit residues: 183.4809 Evaluate side-chains 201 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain R residue 28 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 322 HIS B 225 HIS S 82 GLN R 121 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.108985 restraints weight = 12794.377| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.93 r_work: 0.3342 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8594 Z= 0.167 Angle : 0.566 8.530 11745 Z= 0.298 Chirality : 0.043 0.163 1367 Planarity : 0.004 0.051 1496 Dihedral : 3.992 24.009 1227 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.62 % Allowed : 21.30 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.86 (0.26), residues: 1133 helix: 2.19 (0.26), residues: 396 sheet: -0.04 (0.30), residues: 273 loop : -0.43 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 209 HIS 0.005 0.001 HIS B 225 PHE 0.014 0.001 PHE S 68 TYR 0.016 0.001 TYR S 216 ARG 0.009 0.000 ARG A 230 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 442) hydrogen bonds : angle 4.45732 ( 1245) SS BOND : bond 0.00463 ( 2) SS BOND : angle 0.96061 ( 4) covalent geometry : bond 0.00383 ( 8592) covalent geometry : angle 0.56599 (11741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.867 Fit side-chains REVERT: A 8 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7811 (mt-10) REVERT: A 227 ASP cc_start: 0.7876 (t0) cc_final: 0.7666 (t0) REVERT: B 155 ASN cc_start: 0.8199 (t0) cc_final: 0.7974 (t0) REVERT: B 291 ASP cc_start: 0.6752 (t70) cc_final: 0.6368 (t70) REVERT: S 34 MET cc_start: 0.8265 (mmm) cc_final: 0.7966 (mmm) REVERT: S 83 MET cc_start: 0.7163 (mmm) cc_final: 0.6852 (mmm) REVERT: S 128 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8317 (mtt) REVERT: S 143 VAL cc_start: 0.8658 (p) cc_final: 0.8380 (m) REVERT: S 162 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7533 (tt) REVERT: S 163 TYR cc_start: 0.8156 (m-80) cc_final: 0.7742 (m-80) REVERT: R 70 LEU cc_start: 0.8932 (mt) cc_final: 0.8668 (mm) REVERT: R 125 PHE cc_start: 0.8680 (m-80) cc_final: 0.8274 (m-80) outliers start: 21 outliers final: 17 residues processed: 204 average time/residue: 0.8386 time to fit residues: 186.3778 Evaluate side-chains 211 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 84 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 84 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN R 121 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.121748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107435 restraints weight = 12806.280| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.93 r_work: 0.3317 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8594 Z= 0.212 Angle : 0.600 7.463 11745 Z= 0.317 Chirality : 0.045 0.194 1367 Planarity : 0.004 0.054 1496 Dihedral : 4.225 24.717 1227 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.86 % Allowed : 22.17 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.70 (0.25), residues: 1133 helix: 1.96 (0.26), residues: 397 sheet: -0.09 (0.29), residues: 279 loop : -0.44 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 209 HIS 0.004 0.001 HIS A 322 PHE 0.015 0.002 PHE S 68 TYR 0.017 0.002 TYR R 102 ARG 0.012 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 442) hydrogen bonds : angle 4.63085 ( 1245) SS BOND : bond 0.00601 ( 2) SS BOND : angle 0.89924 ( 4) covalent geometry : bond 0.00489 ( 8592) covalent geometry : angle 0.59989 (11741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.875 Fit side-chains REVERT: A 8 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7787 (mt-10) REVERT: A 227 ASP cc_start: 0.7893 (t0) cc_final: 0.7682 (t0) REVERT: B 155 ASN cc_start: 0.8233 (t0) cc_final: 0.7958 (t0) REVERT: B 291 ASP cc_start: 0.6840 (t70) cc_final: 0.6468 (t70) REVERT: S 5 VAL cc_start: 0.7880 (t) cc_final: 0.7630 (p) REVERT: S 34 MET cc_start: 0.8258 (mmm) cc_final: 0.7981 (mmm) REVERT: S 83 MET cc_start: 0.7270 (mmm) cc_final: 0.7010 (mmm) REVERT: S 128 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8337 (mtt) REVERT: S 143 VAL cc_start: 0.8690 (p) cc_final: 0.8418 (m) REVERT: S 162 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7680 (tt) REVERT: S 163 TYR cc_start: 0.8153 (m-80) cc_final: 0.7831 (m-80) REVERT: R 70 LEU cc_start: 0.8949 (mt) cc_final: 0.8717 (mm) REVERT: R 125 PHE cc_start: 0.8716 (m-80) cc_final: 0.8313 (m-80) REVERT: R 251 TYR cc_start: 0.8471 (t80) cc_final: 0.7855 (t80) outliers start: 23 outliers final: 14 residues processed: 201 average time/residue: 0.8112 time to fit residues: 177.9302 Evaluate side-chains 206 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 84 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 39 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.123148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.108972 restraints weight = 12621.906| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.92 r_work: 0.3350 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8594 Z= 0.144 Angle : 0.572 8.598 11745 Z= 0.301 Chirality : 0.043 0.221 1367 Planarity : 0.004 0.053 1496 Dihedral : 4.098 24.253 1227 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.99 % Allowed : 23.66 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.75 (0.25), residues: 1133 helix: 2.02 (0.26), residues: 398 sheet: -0.16 (0.29), residues: 275 loop : -0.36 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS R 155 PHE 0.015 0.001 PHE A 328 TYR 0.018 0.001 TYR S 216 ARG 0.012 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 442) hydrogen bonds : angle 4.53028 ( 1245) SS BOND : bond 0.00429 ( 2) SS BOND : angle 0.70401 ( 4) covalent geometry : bond 0.00328 ( 8592) covalent geometry : angle 0.57220 (11741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.928 Fit side-chains REVERT: A 8 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 155 ASN cc_start: 0.8188 (t0) cc_final: 0.7918 (t0) REVERT: B 291 ASP cc_start: 0.6753 (t70) cc_final: 0.6374 (t70) REVERT: B 296 VAL cc_start: 0.8463 (m) cc_final: 0.8253 (t) REVERT: S 5 VAL cc_start: 0.7886 (t) cc_final: 0.7627 (p) REVERT: S 34 MET cc_start: 0.8229 (mmm) cc_final: 0.7943 (mmm) REVERT: S 83 MET cc_start: 0.7288 (mmm) cc_final: 0.6962 (mmm) REVERT: S 128 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8365 (mtt) REVERT: S 143 VAL cc_start: 0.8690 (p) cc_final: 0.8415 (m) REVERT: S 163 TYR cc_start: 0.8131 (m-80) cc_final: 0.7815 (m-80) REVERT: R 125 PHE cc_start: 0.8688 (m-80) cc_final: 0.8261 (m-80) REVERT: R 251 TYR cc_start: 0.8418 (t80) cc_final: 0.7860 (t80) outliers start: 16 outliers final: 13 residues processed: 197 average time/residue: 0.8210 time to fit residues: 175.9014 Evaluate side-chains 206 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 84 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 111 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.123823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109518 restraints weight = 12810.907| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.95 r_work: 0.3352 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8594 Z= 0.140 Angle : 0.567 7.408 11745 Z= 0.299 Chirality : 0.043 0.208 1367 Planarity : 0.004 0.051 1496 Dihedral : 4.050 24.013 1227 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.24 % Allowed : 24.03 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.79 (0.26), residues: 1133 helix: 2.06 (0.26), residues: 397 sheet: -0.12 (0.29), residues: 283 loop : -0.35 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS R 155 PHE 0.013 0.001 PHE S 68 TYR 0.018 0.001 TYR S 216 ARG 0.011 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 442) hydrogen bonds : angle 4.50541 ( 1245) SS BOND : bond 0.00539 ( 2) SS BOND : angle 0.70221 ( 4) covalent geometry : bond 0.00318 ( 8592) covalent geometry : angle 0.56712 (11741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6489.65 seconds wall clock time: 112 minutes 21.67 seconds (6741.67 seconds total)