Starting phenix.real_space_refine on Sat Aug 23 02:58:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ije_60629/08_2025/9ije_60629.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ije_60629/08_2025/9ije_60629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ije_60629/08_2025/9ije_60629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ije_60629/08_2025/9ije_60629.map" model { file = "/net/cci-nas-00/data/ceres_data/9ije_60629/08_2025/9ije_60629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ije_60629/08_2025/9ije_60629.cif" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.113 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 61 5.16 5 C 5931 2.51 5 N 1617 2.21 5 O 1731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9340 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2539 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASP:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "N" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 950 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1754 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1886 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 237} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1804 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 393 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {'ALE': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.45, per 1000 atoms: 0.26 Number of scatterers: 9340 At special positions: 0 Unit cell: (89.8475, 123.405, 126.652, 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 61 16.00 O 1731 8.00 N 1617 7.00 C 5931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 229 " 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: 0.99 Conformation dependent library (CDL) restraints added in 378.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 16 sheets defined 36.1% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 1 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.110A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 65 Processing helix chain 'R' and resid 71 through 90 removed outlier: 4.179A pdb=" N PHE R 75 " --> pdb=" O MET R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 101 Processing helix chain 'R' and resid 106 through 141 removed outlier: 3.508A pdb=" N GLU R 111 " --> pdb=" O ALA R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 149 Processing helix chain 'R' and resid 150 through 175 Proline residue: R 172 - end of helix Processing helix chain 'R' and resid 203 through 213 Processing helix chain 'R' and resid 213 through 243 Processing helix chain 'R' and resid 290 through 317 removed outlier: 3.754A pdb=" N PHE R 301 " --> pdb=" O ILE R 297 " (cutoff:3.500A) Proline residue: R 307 - end of helix Processing helix chain 'R' and resid 319 through 323 Processing helix chain 'R' and resid 324 through 337 Processing helix chain 'R' and resid 337 through 347 Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 349 through 362 Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.703A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.756A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.285A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.508A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 340 removed outlier: 3.653A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.581A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.801A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.803A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.600A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.640A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.676A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.755A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.675A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.861A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.338A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'D' and resid 147 through 148 removed outlier: 6.483A pdb=" N VAL D 147 " --> pdb=" O GLU D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 194 through 195 removed outlier: 6.544A pdb=" N TRP D 176 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR D 190 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU D 174 " --> pdb=" O TYR D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 210 through 212 removed outlier: 9.436A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1344 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: 1.68 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1496 1.30 - 1.43: 2563 1.43 - 1.56: 5387 1.56 - 1.69: 2 1.69 - 1.82: 87 Bond restraints: 9535 Sorted by residual: bond pdb=" C3 ALE R 401 " pdb=" O1 ALE R 401 " ideal model delta sigma weight residual 1.353 1.505 -0.152 2.00e-02 2.50e+03 5.81e+01 bond pdb=" C ASP R 117 " pdb=" O ASP R 117 " ideal model delta sigma weight residual 1.236 1.172 0.065 1.15e-02 7.56e+03 3.17e+01 bond pdb=" CA SER B 227 " pdb=" CB SER B 227 " ideal model delta sigma weight residual 1.535 1.480 0.055 1.32e-02 5.74e+03 1.71e+01 bond pdb=" CA SER B 245 " pdb=" CB SER B 245 " ideal model delta sigma weight residual 1.534 1.479 0.056 1.45e-02 4.76e+03 1.48e+01 bond pdb=" C4 ALE R 401 " pdb=" O2 ALE R 401 " ideal model delta sigma weight residual 1.351 1.416 -0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 9530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 12590 1.93 - 3.85: 316 3.85 - 5.78: 40 5.78 - 7.70: 12 7.70 - 9.63: 2 Bond angle restraints: 12960 Sorted by residual: angle pdb=" CA ASP R 117 " pdb=" CB ASP R 117 " pdb=" CG ASP R 117 " ideal model delta sigma weight residual 112.60 119.24 -6.64 1.00e+00 1.00e+00 4.41e+01 angle pdb=" CA GLY R 318 " pdb=" C GLY R 318 " pdb=" O GLY R 318 " ideal model delta sigma weight residual 122.23 118.03 4.20 6.90e-01 2.10e+00 3.71e+01 angle pdb=" CA GLY A 345 " pdb=" C GLY A 345 " pdb=" N ARG A 346 " ideal model delta sigma weight residual 118.46 124.96 -6.50 1.15e+00 7.56e-01 3.19e+01 angle pdb=" C THR C 52 " pdb=" CA THR C 52 " pdb=" CB THR C 52 " ideal model delta sigma weight residual 110.17 104.68 5.49 9.90e-01 1.02e+00 3.07e+01 angle pdb=" CA ASP B 247 " pdb=" CB ASP B 247 " pdb=" CG ASP B 247 " ideal model delta sigma weight residual 112.60 117.90 -5.30 1.00e+00 1.00e+00 2.81e+01 ... (remaining 12955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4962 17.71 - 35.42: 496 35.42 - 53.13: 135 53.13 - 70.83: 34 70.83 - 88.54: 8 Dihedral angle restraints: 5635 sinusoidal: 2095 harmonic: 3540 Sorted by residual: dihedral pdb=" CA GLU D 234 " pdb=" C GLU D 234 " pdb=" N TYR D 235 " pdb=" CA TYR D 235 " ideal model delta harmonic sigma weight residual 180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA LEU A 281 " pdb=" C LEU A 281 " pdb=" N ASN A 282 " pdb=" CA ASN A 282 " ideal model delta harmonic sigma weight residual 180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -118.58 32.58 1 1.00e+01 1.00e-02 1.51e+01 ... (remaining 5632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1443 0.114 - 0.228: 41 0.228 - 0.342: 3 0.342 - 0.456: 0 0.456 - 0.570: 1 Chirality restraints: 1488 Sorted by residual: chirality pdb=" C7 ALE R 401 " pdb=" C1 ALE R 401 " pdb=" C8 ALE R 401 " pdb=" O3 ALE R 401 " both_signs ideal model delta sigma weight residual False 2.28 2.85 -0.57 2.00e-01 2.50e+01 8.13e+00 chirality pdb=" CA THR C 52 " pdb=" N THR C 52 " pdb=" C THR C 52 " pdb=" CB THR C 52 " both_signs ideal model delta sigma weight residual False 2.53 2.79 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA VAL R 323 " pdb=" N VAL R 323 " pdb=" C VAL R 323 " pdb=" CB VAL R 323 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1485 not shown) Planarity restraints: 1648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 74 " -0.064 5.00e-02 4.00e+02 9.47e-02 1.44e+01 pdb=" N PRO D 75 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 92 " 0.056 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO R 93 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO R 93 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 93 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 244 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C GLY B 244 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY B 244 " 0.018 2.00e-02 2.50e+03 pdb=" N SER B 245 " 0.016 2.00e-02 2.50e+03 ... (remaining 1645 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1729 2.77 - 3.30: 8515 3.30 - 3.84: 15752 3.84 - 4.37: 18931 4.37 - 4.90: 33135 Nonbonded interactions: 78062 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.240 3.040 nonbonded pdb=" N GLU A 304 " pdb=" OE1 GLU A 304 " model vdw 2.248 3.120 nonbonded pdb=" O TYR R 204 " pdb=" OG SER R 208 " model vdw 2.272 3.040 nonbonded pdb=" NZ LYS D 163 " pdb=" OE2 GLU D 234 " model vdw 2.274 3.120 nonbonded pdb=" OG SER D 52 " pdb=" OE2 GLU A 21 " model vdw 2.305 3.040 ... (remaining 78057 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.630 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 9539 Z= 0.300 Angle : 0.695 9.626 12968 Z= 0.447 Chirality : 0.050 0.570 1488 Planarity : 0.006 0.105 1648 Dihedral : 15.986 88.544 3345 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.15 % Allowed : 19.61 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.24), residues: 1207 helix: 1.79 (0.25), residues: 393 sheet: 0.85 (0.28), residues: 301 loop : -0.12 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 160 TYR 0.025 0.002 TYR D 235 PHE 0.012 0.001 PHE R 309 TRP 0.011 0.001 TRP R 113 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 9535) covalent geometry : angle 0.69508 (12960) SS BOND : bond 0.00164 ( 4) SS BOND : angle 1.03436 ( 8) hydrogen bonds : bond 0.17047 ( 481) hydrogen bonds : angle 6.49754 ( 1344) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.380 Fit side-chains REVERT: B 189 SER cc_start: 0.9143 (t) cc_final: 0.8916 (p) REVERT: N 83 MET cc_start: 0.8606 (mtp) cc_final: 0.8304 (mtm) REVERT: D 63 THR cc_start: 0.8665 (p) cc_final: 0.8401 (t) REVERT: D 160 ARG cc_start: 0.7182 (ttm-80) cc_final: 0.6949 (ttp80) REVERT: D 186 GLN cc_start: 0.8194 (pt0) cc_final: 0.7839 (pt0) REVERT: D 234 GLU cc_start: 0.8051 (mp0) cc_final: 0.7661 (mp0) REVERT: R 155 ARG cc_start: 0.7091 (ttp-110) cc_final: 0.6157 (mmm160) REVERT: R 333 TRP cc_start: 0.8128 (m100) cc_final: 0.7204 (m-10) REVERT: R 358 ARG cc_start: 0.6732 (mtm110) cc_final: 0.6412 (ttp-110) REVERT: A 254 ASN cc_start: 0.8682 (t0) cc_final: 0.8429 (m-40) REVERT: C 42 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.5931 (mp0) outliers start: 21 outliers final: 12 residues processed: 165 average time/residue: 0.7044 time to fit residues: 123.1015 Evaluate side-chains 147 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 120 GLN D 3 GLN D 77 ASN D 142 GLN D 179 GLN D 183 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 239 ASN A 380 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097386 restraints weight = 11886.408| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.27 r_work: 0.3093 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9539 Z= 0.121 Angle : 0.518 6.903 12968 Z= 0.279 Chirality : 0.042 0.201 1488 Planarity : 0.005 0.067 1648 Dihedral : 5.832 55.055 1360 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.17 % Allowed : 20.02 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.24), residues: 1207 helix: 2.47 (0.25), residues: 387 sheet: 0.84 (0.28), residues: 302 loop : 0.00 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 358 TYR 0.017 0.001 TYR D 235 PHE 0.013 0.001 PHE A 212 TRP 0.011 0.001 TRP B 339 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9535) covalent geometry : angle 0.51821 (12960) SS BOND : bond 0.00277 ( 4) SS BOND : angle 0.68781 ( 8) hydrogen bonds : bond 0.04217 ( 481) hydrogen bonds : angle 4.61870 ( 1344) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: B 10 GLU cc_start: 0.6188 (OUTLIER) cc_final: 0.5890 (tp30) REVERT: B 189 SER cc_start: 0.9073 (t) cc_final: 0.8616 (p) REVERT: B 314 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8174 (ttt180) REVERT: N 1 GLN cc_start: 0.7432 (pm20) cc_final: 0.7217 (pm20) REVERT: N 83 MET cc_start: 0.8770 (mtp) cc_final: 0.8349 (mtm) REVERT: D 18 ARG cc_start: 0.7063 (tpp-160) cc_final: 0.6674 (tpp-160) REVERT: D 186 GLN cc_start: 0.8367 (pt0) cc_final: 0.8158 (pt0) REVERT: D 234 GLU cc_start: 0.8168 (mp0) cc_final: 0.7850 (mp0) REVERT: D 235 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.6570 (m-80) REVERT: R 148 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7950 (mp) REVERT: R 333 TRP cc_start: 0.8137 (m100) cc_final: 0.7011 (m-10) REVERT: C 21 MET cc_start: 0.7110 (tpp) cc_final: 0.6752 (tpt) REVERT: C 42 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: C 58 GLU cc_start: 0.8115 (pt0) cc_final: 0.7587 (pm20) outliers start: 31 outliers final: 12 residues processed: 164 average time/residue: 0.7199 time to fit residues: 124.9952 Evaluate side-chains 151 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 42 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 91 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 45 optimal weight: 0.0060 chunk 20 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 293 ASN N 120 GLN D 3 GLN D 77 ASN D 183 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 380 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.096269 restraints weight = 11805.015| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.16 r_work: 0.3066 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9539 Z= 0.147 Angle : 0.535 6.952 12968 Z= 0.287 Chirality : 0.043 0.221 1488 Planarity : 0.005 0.061 1648 Dihedral : 5.715 57.161 1345 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.58 % Allowed : 20.94 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.24), residues: 1207 helix: 2.39 (0.25), residues: 387 sheet: 0.80 (0.28), residues: 298 loop : -0.04 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 358 TYR 0.020 0.002 TYR D 235 PHE 0.013 0.001 PHE A 212 TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9535) covalent geometry : angle 0.53526 (12960) SS BOND : bond 0.00346 ( 4) SS BOND : angle 0.81855 ( 8) hydrogen bonds : bond 0.04441 ( 481) hydrogen bonds : angle 4.55215 ( 1344) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 189 SER cc_start: 0.8987 (t) cc_final: 0.8453 (p) REVERT: B 314 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8043 (ttt180) REVERT: N 1 GLN cc_start: 0.7500 (pm20) cc_final: 0.7094 (pm20) REVERT: N 83 MET cc_start: 0.8626 (mtp) cc_final: 0.8226 (mtm) REVERT: D 160 ARG cc_start: 0.7412 (mtp-110) cc_final: 0.6937 (ttp-110) REVERT: D 186 GLN cc_start: 0.8265 (pt0) cc_final: 0.8056 (pt0) REVERT: D 235 TYR cc_start: 0.6646 (OUTLIER) cc_final: 0.6175 (t80) REVERT: R 333 TRP cc_start: 0.8050 (m100) cc_final: 0.6912 (m-10) REVERT: C 21 MET cc_start: 0.7046 (tpp) cc_final: 0.6614 (tpt) REVERT: C 47 GLU cc_start: 0.7363 (pm20) cc_final: 0.7133 (pm20) outliers start: 35 outliers final: 19 residues processed: 157 average time/residue: 0.6928 time to fit residues: 115.2213 Evaluate side-chains 149 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 42 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 46 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 120 GLN D 3 GLN D 77 ASN D 183 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.124335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.095750 restraints weight = 11961.293| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.17 r_work: 0.3060 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9539 Z= 0.152 Angle : 0.539 6.823 12968 Z= 0.289 Chirality : 0.043 0.215 1488 Planarity : 0.005 0.058 1648 Dihedral : 5.517 53.545 1345 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.68 % Allowed : 20.12 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.24), residues: 1207 helix: 2.41 (0.26), residues: 388 sheet: 0.73 (0.28), residues: 300 loop : -0.09 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 358 TYR 0.018 0.002 TYR D 235 PHE 0.013 0.002 PHE A 212 TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9535) covalent geometry : angle 0.53837 (12960) SS BOND : bond 0.00320 ( 4) SS BOND : angle 0.82160 ( 8) hydrogen bonds : bond 0.04386 ( 481) hydrogen bonds : angle 4.50920 ( 1344) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 189 SER cc_start: 0.8981 (t) cc_final: 0.8389 (p) REVERT: B 234 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.6741 (t80) REVERT: B 314 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8105 (ttt180) REVERT: N 1 GLN cc_start: 0.7441 (pm20) cc_final: 0.7141 (pm20) REVERT: N 83 MET cc_start: 0.8572 (mtp) cc_final: 0.8263 (mtm) REVERT: D 160 ARG cc_start: 0.7373 (mtp-110) cc_final: 0.6936 (ttp-110) REVERT: D 186 GLN cc_start: 0.8217 (pt0) cc_final: 0.7984 (pt0) REVERT: D 235 TYR cc_start: 0.6613 (OUTLIER) cc_final: 0.6046 (t80) REVERT: R 333 TRP cc_start: 0.8085 (m100) cc_final: 0.6943 (m-10) REVERT: C 21 MET cc_start: 0.7103 (tpp) cc_final: 0.6671 (tpt) REVERT: C 47 GLU cc_start: 0.7347 (pm20) cc_final: 0.7108 (pm20) outliers start: 36 outliers final: 22 residues processed: 162 average time/residue: 0.6589 time to fit residues: 113.3164 Evaluate side-chains 159 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 42 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 38 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 293 ASN N 120 GLN D 3 GLN D 183 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097374 restraints weight = 12032.910| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.16 r_work: 0.3092 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9539 Z= 0.111 Angle : 0.497 6.334 12968 Z= 0.265 Chirality : 0.041 0.193 1488 Planarity : 0.005 0.063 1648 Dihedral : 5.210 53.079 1345 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.19 % Allowed : 19.71 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.24), residues: 1207 helix: 2.63 (0.26), residues: 388 sheet: 0.79 (0.28), residues: 300 loop : -0.06 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 358 TYR 0.016 0.001 TYR D 235 PHE 0.013 0.001 PHE A 212 TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9535) covalent geometry : angle 0.49645 (12960) SS BOND : bond 0.00280 ( 4) SS BOND : angle 0.70608 ( 8) hydrogen bonds : bond 0.03773 ( 481) hydrogen bonds : angle 4.27450 ( 1344) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.8478 (pp-130) cc_final: 0.8163 (pp-130) REVERT: B 234 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.6855 (t80) REVERT: N 1 GLN cc_start: 0.7451 (pm20) cc_final: 0.7104 (pm20) REVERT: N 83 MET cc_start: 0.8601 (mtp) cc_final: 0.8277 (mtm) REVERT: D 160 ARG cc_start: 0.7340 (mtp-110) cc_final: 0.6892 (ttp-110) REVERT: D 234 GLU cc_start: 0.8127 (mp0) cc_final: 0.7702 (mp0) REVERT: D 235 TYR cc_start: 0.6499 (OUTLIER) cc_final: 0.5978 (t80) REVERT: R 151 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7025 (ttmm) REVERT: R 333 TRP cc_start: 0.8010 (m100) cc_final: 0.6790 (m-10) REVERT: C 21 MET cc_start: 0.7077 (tpp) cc_final: 0.6648 (tpt) REVERT: C 42 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: C 47 GLU cc_start: 0.7396 (pm20) cc_final: 0.7191 (pm20) outliers start: 41 outliers final: 26 residues processed: 164 average time/residue: 0.7117 time to fit residues: 123.3522 Evaluate side-chains 162 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 118 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 120 GLN D 3 GLN D 77 ASN D 169 ASN D 183 GLN D 186 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.124748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096274 restraints weight = 12005.387| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.18 r_work: 0.3068 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9539 Z= 0.139 Angle : 0.527 6.544 12968 Z= 0.281 Chirality : 0.042 0.199 1488 Planarity : 0.005 0.063 1648 Dihedral : 5.406 52.153 1345 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.29 % Allowed : 20.12 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.24), residues: 1207 helix: 2.54 (0.26), residues: 388 sheet: 0.77 (0.28), residues: 298 loop : -0.06 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 358 TYR 0.015 0.002 TYR D 235 PHE 0.013 0.001 PHE A 212 TRP 0.012 0.002 TRP A 234 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9535) covalent geometry : angle 0.52608 (12960) SS BOND : bond 0.00304 ( 4) SS BOND : angle 1.11133 ( 8) hydrogen bonds : bond 0.04173 ( 481) hydrogen bonds : angle 4.39785 ( 1344) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.8441 (pp-130) cc_final: 0.8182 (pp-130) REVERT: B 234 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.6752 (t80) REVERT: B 314 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8051 (ttt180) REVERT: N 1 GLN cc_start: 0.7450 (pm20) cc_final: 0.7072 (pm20) REVERT: N 83 MET cc_start: 0.8541 (mtp) cc_final: 0.8267 (mtm) REVERT: D 160 ARG cc_start: 0.7311 (mtp-110) cc_final: 0.6897 (ttp-110) REVERT: D 235 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.6036 (t80) REVERT: R 151 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7069 (ttmm) REVERT: R 333 TRP cc_start: 0.8077 (m100) cc_final: 0.6885 (m-10) REVERT: C 21 MET cc_start: 0.7134 (tpp) cc_final: 0.6650 (tpt) REVERT: C 42 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: C 47 GLU cc_start: 0.7503 (pm20) cc_final: 0.7294 (pm20) outliers start: 42 outliers final: 30 residues processed: 166 average time/residue: 0.6553 time to fit residues: 115.7834 Evaluate side-chains 169 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 293 ASN N 120 GLN D 3 GLN D 77 ASN D 183 GLN D 186 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.125205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.096697 restraints weight = 12135.790| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.17 r_work: 0.3084 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9539 Z= 0.121 Angle : 0.510 6.514 12968 Z= 0.271 Chirality : 0.041 0.194 1488 Planarity : 0.005 0.063 1648 Dihedral : 5.248 51.884 1345 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.98 % Allowed : 20.43 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.24), residues: 1207 helix: 2.62 (0.26), residues: 388 sheet: 0.80 (0.28), residues: 298 loop : -0.04 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 358 TYR 0.016 0.001 TYR D 235 PHE 0.013 0.001 PHE A 212 TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9535) covalent geometry : angle 0.50922 (12960) SS BOND : bond 0.00278 ( 4) SS BOND : angle 0.94668 ( 8) hydrogen bonds : bond 0.03876 ( 481) hydrogen bonds : angle 4.29185 ( 1344) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.6729 (t80) REVERT: N 1 GLN cc_start: 0.7435 (pm20) cc_final: 0.7076 (pm20) REVERT: N 83 MET cc_start: 0.8579 (mtp) cc_final: 0.8265 (mtm) REVERT: D 89 GLU cc_start: 0.8141 (mp0) cc_final: 0.7866 (pp20) REVERT: D 160 ARG cc_start: 0.7269 (mtp-110) cc_final: 0.6863 (ttp-110) REVERT: D 235 TYR cc_start: 0.6520 (OUTLIER) cc_final: 0.6036 (t80) REVERT: R 151 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7046 (ttmm) REVERT: R 333 TRP cc_start: 0.8052 (m100) cc_final: 0.6839 (m-10) REVERT: C 21 MET cc_start: 0.7128 (tpp) cc_final: 0.6647 (tpt) REVERT: C 42 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: C 46 LYS cc_start: 0.8180 (tppp) cc_final: 0.7402 (ptpp) outliers start: 39 outliers final: 31 residues processed: 164 average time/residue: 0.6432 time to fit residues: 111.7533 Evaluate side-chains 168 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 82 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 120 GLN D 3 GLN D 183 GLN D 186 GLN A 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.095808 restraints weight = 12004.693| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.16 r_work: 0.3072 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9539 Z= 0.135 Angle : 0.527 6.872 12968 Z= 0.280 Chirality : 0.042 0.198 1488 Planarity : 0.005 0.063 1648 Dihedral : 5.376 51.628 1345 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.09 % Allowed : 20.33 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.24), residues: 1207 helix: 2.55 (0.26), residues: 388 sheet: 0.81 (0.28), residues: 297 loop : -0.07 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 358 TYR 0.016 0.002 TYR D 235 PHE 0.012 0.001 PHE A 212 TRP 0.013 0.002 TRP A 234 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9535) covalent geometry : angle 0.52677 (12960) SS BOND : bond 0.00280 ( 4) SS BOND : angle 0.96416 ( 8) hydrogen bonds : bond 0.04115 ( 481) hydrogen bonds : angle 4.37717 ( 1344) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.6740 (t80) REVERT: B 314 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8095 (ttt180) REVERT: N 1 GLN cc_start: 0.7387 (pm20) cc_final: 0.7013 (pm20) REVERT: N 83 MET cc_start: 0.8473 (mtp) cc_final: 0.8164 (mtm) REVERT: D 89 GLU cc_start: 0.8184 (mp0) cc_final: 0.7757 (pp20) REVERT: D 160 ARG cc_start: 0.7266 (mtp-110) cc_final: 0.6860 (ttp-110) REVERT: D 235 TYR cc_start: 0.6531 (OUTLIER) cc_final: 0.5983 (t80) REVERT: R 151 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7035 (ttmm) REVERT: R 333 TRP cc_start: 0.8059 (m100) cc_final: 0.6880 (m-10) REVERT: C 21 MET cc_start: 0.7126 (tpp) cc_final: 0.6645 (tpt) REVERT: C 42 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: C 46 LYS cc_start: 0.8250 (tppp) cc_final: 0.7524 (ptpp) outliers start: 40 outliers final: 31 residues processed: 164 average time/residue: 0.6076 time to fit residues: 105.9220 Evaluate side-chains 172 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 0 optimal weight: 20.0000 chunk 120 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 120 GLN D 3 GLN D 77 ASN D 183 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.098194 restraints weight = 12021.155| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.27 r_work: 0.3107 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9539 Z= 0.100 Angle : 0.491 7.007 12968 Z= 0.260 Chirality : 0.040 0.177 1488 Planarity : 0.005 0.060 1648 Dihedral : 4.780 47.186 1343 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.58 % Allowed : 20.84 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.24), residues: 1207 helix: 2.77 (0.26), residues: 388 sheet: 0.74 (0.28), residues: 303 loop : -0.03 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 358 TYR 0.015 0.001 TYR D 235 PHE 0.012 0.001 PHE A 212 TRP 0.012 0.001 TRP A 234 HIS 0.002 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 9535) covalent geometry : angle 0.49054 (12960) SS BOND : bond 0.00234 ( 4) SS BOND : angle 0.70379 ( 8) hydrogen bonds : bond 0.03483 ( 481) hydrogen bonds : angle 4.13487 ( 1344) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.8558 (pp-130) cc_final: 0.8220 (pp-130) REVERT: B 234 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.6936 (t80) REVERT: N 1 GLN cc_start: 0.7521 (pm20) cc_final: 0.7175 (pm20) REVERT: N 80 TYR cc_start: 0.8691 (m-80) cc_final: 0.8357 (m-80) REVERT: N 83 MET cc_start: 0.8744 (mtp) cc_final: 0.8459 (mtm) REVERT: D 89 GLU cc_start: 0.8102 (mp0) cc_final: 0.7725 (pp20) REVERT: D 160 ARG cc_start: 0.7368 (mtp-110) cc_final: 0.6978 (ttp-110) REVERT: D 234 GLU cc_start: 0.8125 (mp0) cc_final: 0.7739 (mp0) REVERT: D 235 TYR cc_start: 0.6424 (OUTLIER) cc_final: 0.5911 (t80) REVERT: R 151 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7131 (ttmm) REVERT: R 333 TRP cc_start: 0.8150 (m100) cc_final: 0.7027 (m-10) REVERT: A 25 MET cc_start: 0.7644 (mmm) cc_final: 0.7259 (mtp) REVERT: A 346 ARG cc_start: 0.7225 (ptp-110) cc_final: 0.6400 (ptp-110) REVERT: C 42 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: C 46 LYS cc_start: 0.8275 (tppp) cc_final: 0.7539 (ptpp) outliers start: 35 outliers final: 28 residues processed: 164 average time/residue: 0.6636 time to fit residues: 115.6806 Evaluate side-chains 169 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 77 ASN N 120 GLN D 3 GLN D 183 GLN A 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.095595 restraints weight = 11885.361| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.19 r_work: 0.3065 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9539 Z= 0.148 Angle : 0.542 7.553 12968 Z= 0.288 Chirality : 0.042 0.197 1488 Planarity : 0.005 0.061 1648 Dihedral : 5.251 48.127 1343 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.68 % Allowed : 20.94 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.24), residues: 1207 helix: 2.52 (0.26), residues: 388 sheet: 0.75 (0.28), residues: 299 loop : -0.02 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 358 TYR 0.015 0.002 TYR D 235 PHE 0.013 0.001 PHE A 212 TRP 0.013 0.002 TRP A 234 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9535) covalent geometry : angle 0.54121 (12960) SS BOND : bond 0.00299 ( 4) SS BOND : angle 0.93745 ( 8) hydrogen bonds : bond 0.04250 ( 481) hydrogen bonds : angle 4.40407 ( 1344) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.6802 (t80) REVERT: B 314 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8424 (ttt180) REVERT: N 1 GLN cc_start: 0.7414 (pm20) cc_final: 0.7038 (pm20) REVERT: N 80 TYR cc_start: 0.8685 (m-80) cc_final: 0.8338 (m-80) REVERT: N 83 MET cc_start: 0.8576 (mtp) cc_final: 0.8292 (mtm) REVERT: D 89 GLU cc_start: 0.8113 (mp0) cc_final: 0.7745 (pp20) REVERT: D 160 ARG cc_start: 0.7296 (mtp-110) cc_final: 0.6892 (ttp-110) REVERT: D 202 ARG cc_start: 0.7326 (mtm-85) cc_final: 0.7036 (mtm180) REVERT: D 235 TYR cc_start: 0.6531 (OUTLIER) cc_final: 0.5932 (t80) REVERT: R 151 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7076 (ttmm) REVERT: R 291 LEU cc_start: 0.8318 (tp) cc_final: 0.8074 (tp) REVERT: R 333 TRP cc_start: 0.8095 (m100) cc_final: 0.6928 (m-10) REVERT: C 42 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: C 46 LYS cc_start: 0.8303 (tppp) cc_final: 0.7575 (ptpp) outliers start: 36 outliers final: 26 residues processed: 166 average time/residue: 0.6873 time to fit residues: 121.1393 Evaluate side-chains 170 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 313 VAL Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 22 optimal weight: 3.9990 chunk 120 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 0.0170 chunk 25 optimal weight: 5.9990 overall best weight: 1.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 293 ASN N 77 ASN N 120 GLN D 3 GLN D 77 ASN D 183 GLN A 236 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095687 restraints weight = 11793.282| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.19 r_work: 0.3066 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9539 Z= 0.146 Angle : 0.542 7.340 12968 Z= 0.288 Chirality : 0.042 0.209 1488 Planarity : 0.005 0.061 1648 Dihedral : 5.247 47.899 1343 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.47 % Allowed : 21.35 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.24), residues: 1207 helix: 2.48 (0.26), residues: 388 sheet: 0.74 (0.28), residues: 299 loop : -0.06 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 358 TYR 0.016 0.002 TYR D 235 PHE 0.013 0.001 PHE A 212 TRP 0.012 0.002 TRP A 234 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9535) covalent geometry : angle 0.54184 (12960) SS BOND : bond 0.00301 ( 4) SS BOND : angle 0.93816 ( 8) hydrogen bonds : bond 0.04185 ( 481) hydrogen bonds : angle 4.39202 ( 1344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4745.87 seconds wall clock time: 81 minutes 34.35 seconds (4894.35 seconds total)