Starting phenix.real_space_refine on Wed Jan 14 00:20:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f1o_31421/01_2026/7f1o_31421.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f1o_31421/01_2026/7f1o_31421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7f1o_31421/01_2026/7f1o_31421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f1o_31421/01_2026/7f1o_31421.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f1o_31421/01_2026/7f1o_31421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f1o_31421/01_2026/7f1o_31421.map" } resolution = 3.13 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= -0.002 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3052 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 55 5.16 5 C 5199 2.51 5 N 1438 2.21 5 O 1513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8208 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2208 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 9, 'TRANS': 267} Chain breaks: 3 Chain: "A" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1937 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2619 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Conformer: "B" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} bond proxies already assigned to first conformer: 2640 Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ACYS B 233 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 233 " occ=0.50 residue: pdb=" N ACYS B 271 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 271 " occ=0.50 Time building chain proxies: 2.25, per 1000 atoms: 0.27 Number of scatterers: 8208 At special positions: 0 Unit cell: (78.264, 98.917, 127.179, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 2 15.00 Mg 1 11.99 O 1513 8.00 N 1438 7.00 C 5199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 399.3 milliseconds 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 44.9% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'F' and resid 20 through 51 Processing helix chain 'F' and resid 58 through 88 Proline residue: F 79 - end of helix Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 95 through 127 removed outlier: 3.593A pdb=" N ASN F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 135 Processing helix chain 'F' and resid 136 through 161 Proline residue: F 158 - end of helix Processing helix chain 'F' and resid 191 through 237 Proline residue: F 206 - end of helix Processing helix chain 'F' and resid 265 through 299 Proline residue: F 287 - end of helix Proline residue: F 296 - end of helix Processing helix chain 'F' and resid 309 through 332 Proline residue: F 328 - end of helix Processing helix chain 'F' and resid 334 through 346 Processing helix chain 'A' and resid 13 through 39 Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.558A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 353 Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.860A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.591A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.540A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 9.276A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.714A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.819A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.854A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.685A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.649A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.579A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.193A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 4.600A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1281 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: 1.18 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1319 1.27 - 1.41: 2217 1.41 - 1.55: 4767 1.55 - 1.69: 3 1.69 - 1.84: 74 Bond restraints: 8380 Sorted by residual: bond pdb=" CA PHE F 203 " pdb=" C PHE F 203 " ideal model delta sigma weight residual 1.524 1.354 0.169 1.29e-02 6.01e+03 1.72e+02 bond pdb=" C VAL F 200 " pdb=" O VAL F 200 " ideal model delta sigma weight residual 1.237 1.130 0.107 1.13e-02 7.83e+03 8.89e+01 bond pdb=" CA VAL F 200 " pdb=" C VAL F 200 " ideal model delta sigma weight residual 1.524 1.421 0.103 1.22e-02 6.72e+03 7.16e+01 bond pdb=" CA SER F 199 " pdb=" C SER F 199 " ideal model delta sigma weight residual 1.524 1.417 0.107 1.27e-02 6.20e+03 7.09e+01 bond pdb=" CA TYR F 194 " pdb=" C TYR F 194 " ideal model delta sigma weight residual 1.523 1.416 0.107 1.30e-02 5.92e+03 6.79e+01 ... (remaining 8375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 11188 3.51 - 7.01: 141 7.01 - 10.52: 20 10.52 - 14.02: 5 14.02 - 17.53: 2 Bond angle restraints: 11356 Sorted by residual: angle pdb=" C ILE F 205 " pdb=" N PRO F 206 " pdb=" CA PRO F 206 " ideal model delta sigma weight residual 119.05 103.76 15.29 1.11e+00 8.12e-01 1.90e+02 angle pdb=" N CYS A 365 " pdb=" CA CYS A 365 " pdb=" C CYS A 365 " ideal model delta sigma weight residual 109.50 91.97 17.53 1.58e+00 4.01e-01 1.23e+02 angle pdb=" N TYR F 194 " pdb=" CA TYR F 194 " pdb=" C TYR F 194 " ideal model delta sigma weight residual 111.28 100.71 10.57 1.09e+00 8.42e-01 9.40e+01 angle pdb=" CA VAL F 200 " pdb=" C VAL F 200 " pdb=" O VAL F 200 " ideal model delta sigma weight residual 121.17 111.87 9.30 1.06e+00 8.90e-01 7.70e+01 angle pdb=" N SER F 199 " pdb=" CA SER F 199 " pdb=" C SER F 199 " ideal model delta sigma weight residual 111.07 101.78 9.29 1.07e+00 8.73e-01 7.54e+01 ... (remaining 11351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4405 17.79 - 35.58: 468 35.58 - 53.38: 79 53.38 - 71.17: 20 71.17 - 88.96: 9 Dihedral angle restraints: 4981 sinusoidal: 1962 harmonic: 3019 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual 93.00 9.54 83.46 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" N TYR F 204 " pdb=" C TYR F 204 " pdb=" CA TYR F 204 " pdb=" CB TYR F 204 " ideal model delta harmonic sigma weight residual 122.80 138.63 -15.83 0 2.50e+00 1.60e-01 4.01e+01 dihedral pdb=" C ILE F 205 " pdb=" N ILE F 205 " pdb=" CA ILE F 205 " pdb=" CB ILE F 205 " ideal model delta harmonic sigma weight residual -122.00 -137.26 15.26 0 2.50e+00 1.60e-01 3.73e+01 ... (remaining 4978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 1242 0.167 - 0.333: 20 0.333 - 0.499: 10 0.499 - 0.666: 1 0.666 - 0.832: 2 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA TYR F 204 " pdb=" N TYR F 204 " pdb=" C TYR F 204 " pdb=" CB TYR F 204 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" CA PRO F 206 " pdb=" N PRO F 206 " pdb=" C PRO F 206 " pdb=" CB PRO F 206 " both_signs ideal model delta sigma weight residual False 2.72 2.01 0.71 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CA ILE F 205 " pdb=" N ILE F 205 " pdb=" C ILE F 205 " pdb=" CB ILE F 205 " both_signs ideal model delta sigma weight residual False 2.43 1.84 0.59 2.00e-01 2.50e+01 8.85e+00 ... (remaining 1272 not shown) Planarity restraints: 1441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 205 " 0.134 5.00e-02 4.00e+02 2.02e-01 6.55e+01 pdb=" N PRO F 206 " -0.350 5.00e-02 4.00e+02 pdb=" CA PRO F 206 " 0.099 5.00e-02 4.00e+02 pdb=" CD PRO F 206 " 0.117 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 200 " 0.039 2.00e-02 2.50e+03 7.63e-02 5.83e+01 pdb=" C VAL F 200 " -0.132 2.00e-02 2.50e+03 pdb=" O VAL F 200 " 0.048 2.00e-02 2.50e+03 pdb=" N ILE F 201 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 201 " 0.039 2.00e-02 2.50e+03 7.30e-02 5.33e+01 pdb=" C ILE F 201 " -0.126 2.00e-02 2.50e+03 pdb=" O ILE F 201 " 0.045 2.00e-02 2.50e+03 pdb=" N SER F 202 " 0.043 2.00e-02 2.50e+03 ... (remaining 1438 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 219 2.65 - 3.21: 8009 3.21 - 3.77: 12728 3.77 - 4.34: 17646 4.34 - 4.90: 29498 Nonbonded interactions: 68100 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.086 3.040 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.094 3.120 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.144 3.040 nonbonded pdb="MG MG A 401 " pdb=" O2B GDP A 402 " model vdw 2.160 2.170 nonbonded pdb=" O ALA A 48 " pdb=" OG SER A 51 " model vdw 2.199 3.040 ... (remaining 68095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.060 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.011 0.169 8383 Z= 0.650 Angle : 1.077 17.527 11362 Z= 0.682 Chirality : 0.078 0.832 1275 Planarity : 0.009 0.202 1441 Dihedral : 15.203 88.962 3014 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.81 % Allowed : 10.40 % Favored : 87.80 % Cbeta Deviations : 0.31 % 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 are not related in a simple way. whole: -2.35 (0.23), residues: 1023 helix: -1.49 (0.22), residues: 416 sheet: -1.18 (0.31), residues: 233 loop : -1.60 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 13 TYR 0.023 0.002 TYR B 59 PHE 0.029 0.003 PHE F 333 TRP 0.015 0.002 TRP A 234 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.01101 ( 8380) covalent geometry : angle 1.07652 (11356) SS BOND : bond 0.00636 ( 3) SS BOND : angle 1.73042 ( 6) hydrogen bonds : bond 0.14768 ( 453) hydrogen bonds : angle 6.93055 ( 1281) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 163 TRP cc_start: 0.7953 (m-10) cc_final: 0.7724 (m-10) REVERT: A 213 GLN cc_start: 0.8245 (mt0) cc_final: 0.8017 (mt0) REVERT: A 265 ARG cc_start: 0.8218 (mmm-85) cc_final: 0.8009 (mtp85) REVERT: A 307 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8049 (mtmm) REVERT: A 368 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7867 (m-30) REVERT: A 392 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7888 (mm-30) REVERT: B 46 ARG cc_start: 0.7678 (mtp-110) cc_final: 0.7326 (ttp80) REVERT: B 59 TYR cc_start: 0.7670 (m-10) cc_final: 0.6233 (m-80) REVERT: B 76 ASP cc_start: 0.7938 (p0) cc_final: 0.7658 (p0) REVERT: B 175 GLN cc_start: 0.8403 (mm110) cc_final: 0.7996 (mp10) REVERT: B 214 ARG cc_start: 0.7854 (mtm180) cc_final: 0.7410 (ptt-90) REVERT: B 262 MET cc_start: 0.7502 (ttt) cc_final: 0.7109 (ttt) REVERT: E 46 GLU cc_start: 0.8126 (tt0) cc_final: 0.7901 (tt0) REVERT: E 105 ARG cc_start: 0.7334 (mpt180) cc_final: 0.6998 (mtp180) outliers start: 15 outliers final: 7 residues processed: 182 average time/residue: 0.1089 time to fit residues: 25.9796 Evaluate side-chains 136 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 206 PRO Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 113 ASN F 164 HIS ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 390 GLN B 75 GLN B 91 HIS B 259 GLN B 340 ASN D 59 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.168344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.125634 restraints weight = 27801.711| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 4.46 r_work: 0.3458 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8383 Z= 0.143 Angle : 0.610 12.076 11362 Z= 0.324 Chirality : 0.044 0.141 1275 Planarity : 0.004 0.039 1441 Dihedral : 6.115 59.144 1157 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.94 % Allowed : 15.59 % Favored : 81.47 % 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 are not related in a simple way. whole: -0.43 (0.25), residues: 1023 helix: 0.65 (0.24), residues: 412 sheet: -0.69 (0.32), residues: 230 loop : -0.91 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 226 TYR 0.010 0.001 TYR F 204 PHE 0.014 0.001 PHE B 199 TRP 0.021 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8380) covalent geometry : angle 0.61024 (11356) SS BOND : bond 0.00296 ( 3) SS BOND : angle 0.96210 ( 6) hydrogen bonds : bond 0.05435 ( 453) hydrogen bonds : angle 5.18376 ( 1281) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 163 TRP cc_start: 0.8132 (m-10) cc_final: 0.7794 (m-10) REVERT: F 226 ARG cc_start: 0.7389 (mtm110) cc_final: 0.7163 (ptp-110) REVERT: F 333 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7631 (m-10) REVERT: A 209 GLU cc_start: 0.7526 (tt0) cc_final: 0.6856 (tt0) REVERT: A 318 TYR cc_start: 0.8153 (t80) cc_final: 0.7616 (t80) REVERT: A 339 TYR cc_start: 0.8393 (m-80) cc_final: 0.8189 (m-80) REVERT: A 356 ARG cc_start: 0.8724 (mtm180) cc_final: 0.8422 (ttp-110) REVERT: B 46 ARG cc_start: 0.8122 (mtp-110) cc_final: 0.7786 (ttp80) REVERT: B 55 LEU cc_start: 0.8380 (mt) cc_final: 0.8144 (mt) REVERT: B 59 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.6761 (m-80) REVERT: B 175 GLN cc_start: 0.8376 (mm110) cc_final: 0.7889 (mp10) REVERT: B 214 ARG cc_start: 0.8366 (mtm180) cc_final: 0.7866 (mtm180) REVERT: B 262 MET cc_start: 0.7578 (ttt) cc_final: 0.7328 (ttt) REVERT: D 59 ASN cc_start: 0.7198 (OUTLIER) cc_final: 0.6848 (t0) REVERT: E 31 ASN cc_start: 0.8042 (m-40) cc_final: 0.7748 (m110) REVERT: E 32 TYR cc_start: 0.8440 (m-80) cc_final: 0.8220 (m-80) REVERT: E 105 ARG cc_start: 0.7431 (mpt180) cc_final: 0.6848 (mtp180) outliers start: 25 outliers final: 17 residues processed: 171 average time/residue: 0.1037 time to fit residues: 23.5893 Evaluate side-chains 157 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 283 CYS Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 HIS ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN D 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.167895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.125233 restraints weight = 31472.324| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 4.86 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8383 Z= 0.145 Angle : 0.567 12.008 11362 Z= 0.300 Chirality : 0.043 0.158 1275 Planarity : 0.004 0.039 1441 Dihedral : 5.404 51.875 1147 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.07 % Allowed : 16.50 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.26), residues: 1023 helix: 1.55 (0.25), residues: 417 sheet: -0.51 (0.32), residues: 234 loop : -0.62 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 317 TYR 0.007 0.001 TYR A 37 PHE 0.014 0.001 PHE E 29 TRP 0.018 0.001 TRP B 169 HIS 0.007 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8380) covalent geometry : angle 0.56733 (11356) SS BOND : bond 0.00182 ( 3) SS BOND : angle 0.78771 ( 6) hydrogen bonds : bond 0.05007 ( 453) hydrogen bonds : angle 4.85112 ( 1281) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 163 TRP cc_start: 0.8007 (m-10) cc_final: 0.7712 (m-10) REVERT: F 333 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7679 (m-10) REVERT: A 16 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7964 (mt-10) REVERT: A 318 TYR cc_start: 0.8083 (t80) cc_final: 0.7746 (t80) REVERT: A 356 ARG cc_start: 0.8582 (mtm180) cc_final: 0.8185 (ttp-110) REVERT: A 392 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7790 (mm-30) REVERT: B 46 ARG cc_start: 0.7672 (mtp-110) cc_final: 0.7298 (ttp80) REVERT: B 59 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.6493 (m-80) REVERT: B 175 GLN cc_start: 0.8344 (mm110) cc_final: 0.7797 (mp10) REVERT: B 217 MET cc_start: 0.6987 (mmm) cc_final: 0.6721 (tpp) REVERT: B 228 ASP cc_start: 0.8304 (m-30) cc_final: 0.8102 (m-30) REVERT: B 262 MET cc_start: 0.7504 (ttt) cc_final: 0.7214 (ttt) REVERT: D 59 ASN cc_start: 0.7257 (OUTLIER) cc_final: 0.6561 (t0) REVERT: E 31 ASN cc_start: 0.7769 (m-40) cc_final: 0.7469 (m110) REVERT: E 105 ARG cc_start: 0.7350 (mpt180) cc_final: 0.6804 (mtp180) outliers start: 35 outliers final: 27 residues processed: 163 average time/residue: 0.0920 time to fit residues: 20.5158 Evaluate side-chains 150 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 283 CYS Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.168620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126842 restraints weight = 22546.977| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 4.03 r_work: 0.3493 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8383 Z= 0.132 Angle : 0.567 11.745 11362 Z= 0.295 Chirality : 0.043 0.158 1275 Planarity : 0.004 0.039 1441 Dihedral : 5.209 48.091 1146 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.95 % Allowed : 17.51 % Favored : 78.53 % 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 are not related in a simple way. whole: 0.71 (0.26), residues: 1023 helix: 1.84 (0.25), residues: 417 sheet: -0.24 (0.33), residues: 222 loop : -0.54 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 226 TYR 0.007 0.001 TYR A 37 PHE 0.013 0.001 PHE E 29 TRP 0.017 0.001 TRP B 169 HIS 0.010 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8380) covalent geometry : angle 0.56692 (11356) SS BOND : bond 0.00405 ( 3) SS BOND : angle 1.07376 ( 6) hydrogen bonds : bond 0.04770 ( 453) hydrogen bonds : angle 4.67325 ( 1281) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 163 TRP cc_start: 0.8126 (m-10) cc_final: 0.7881 (m-10) REVERT: F 306 PHE cc_start: 0.6707 (p90) cc_final: 0.6447 (p90) REVERT: F 333 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7527 (m-10) REVERT: A 16 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8092 (mt-10) REVERT: A 309 GLU cc_start: 0.8727 (pm20) cc_final: 0.8398 (pm20) REVERT: A 392 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8093 (mm-30) REVERT: B 59 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.6868 (m-80) REVERT: B 175 GLN cc_start: 0.8467 (mm110) cc_final: 0.7964 (mp10) REVERT: B 228 ASP cc_start: 0.8271 (m-30) cc_final: 0.7970 (m-30) REVERT: B 262 MET cc_start: 0.7621 (ttt) cc_final: 0.7288 (ttt) REVERT: D 59 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.6744 (t0) REVERT: E 31 ASN cc_start: 0.7952 (m-40) cc_final: 0.7559 (m110) REVERT: E 105 ARG cc_start: 0.7399 (mpt180) cc_final: 0.6870 (mtp180) outliers start: 34 outliers final: 27 residues processed: 157 average time/residue: 0.0918 time to fit residues: 19.9180 Evaluate side-chains 151 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 283 CYS Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 HIS ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN D 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.165367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123853 restraints weight = 28107.207| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 4.24 r_work: 0.3429 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8383 Z= 0.173 Angle : 0.591 11.918 11362 Z= 0.307 Chirality : 0.044 0.158 1275 Planarity : 0.004 0.042 1441 Dihedral : 5.205 48.106 1146 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.65 % Allowed : 16.50 % Favored : 77.85 % 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 are not related in a simple way. whole: 0.84 (0.26), residues: 1023 helix: 1.90 (0.25), residues: 417 sheet: -0.10 (0.33), residues: 221 loop : -0.47 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 265 TYR 0.010 0.001 TYR F 131 PHE 0.014 0.001 PHE F 333 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8380) covalent geometry : angle 0.59047 (11356) SS BOND : bond 0.00293 ( 3) SS BOND : angle 1.02929 ( 6) hydrogen bonds : bond 0.04953 ( 453) hydrogen bonds : angle 4.68073 ( 1281) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 163 TRP cc_start: 0.8186 (m-10) cc_final: 0.7905 (m-10) REVERT: F 306 PHE cc_start: 0.6773 (p90) cc_final: 0.6566 (p90) REVERT: F 333 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7617 (m-10) REVERT: A 211 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.7994 (mttm) REVERT: B 175 GLN cc_start: 0.8475 (mm110) cc_final: 0.7966 (mp10) REVERT: B 214 ARG cc_start: 0.8141 (mtm180) cc_final: 0.7912 (mtm180) REVERT: B 217 MET cc_start: 0.7370 (tpp) cc_final: 0.7078 (tpp) REVERT: B 228 ASP cc_start: 0.8378 (m-30) cc_final: 0.7965 (m-30) REVERT: B 262 MET cc_start: 0.7644 (ttt) cc_final: 0.7148 (ttt) REVERT: D 59 ASN cc_start: 0.7244 (OUTLIER) cc_final: 0.6606 (t0) REVERT: E 31 ASN cc_start: 0.8007 (m-40) cc_final: 0.7554 (m110) outliers start: 49 outliers final: 36 residues processed: 156 average time/residue: 0.0888 time to fit residues: 19.3303 Evaluate side-chains 162 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 283 CYS Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 0.0570 chunk 66 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 98 optimal weight: 0.0000 chunk 60 optimal weight: 0.7980 overall best weight: 0.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.170046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.128423 restraints weight = 23518.264| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 4.12 r_work: 0.3503 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8383 Z= 0.113 Angle : 0.539 11.250 11362 Z= 0.281 Chirality : 0.042 0.142 1275 Planarity : 0.003 0.037 1441 Dihedral : 4.984 42.839 1146 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.16 % Allowed : 19.66 % Favored : 77.18 % 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 are not related in a simple way. whole: 1.05 (0.26), residues: 1023 helix: 2.16 (0.25), residues: 417 sheet: 0.03 (0.33), residues: 215 loop : -0.47 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.019 0.001 TYR A 318 PHE 0.011 0.001 PHE E 29 TRP 0.019 0.001 TRP B 169 HIS 0.003 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8380) covalent geometry : angle 0.53876 (11356) SS BOND : bond 0.00205 ( 3) SS BOND : angle 0.76430 ( 6) hydrogen bonds : bond 0.04385 ( 453) hydrogen bonds : angle 4.49866 ( 1281) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 126 SER cc_start: 0.8685 (m) cc_final: 0.8483 (t) REVERT: F 163 TRP cc_start: 0.8148 (m-10) cc_final: 0.7890 (m-10) REVERT: F 333 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7465 (m-10) REVERT: A 20 ARG cc_start: 0.7989 (ttm110) cc_final: 0.7643 (mtm110) REVERT: A 211 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8004 (mttm) REVERT: A 242 THR cc_start: 0.8679 (m) cc_final: 0.8466 (p) REVERT: A 281 TRP cc_start: 0.8804 (m100) cc_final: 0.8550 (m100) REVERT: B 111 TYR cc_start: 0.8729 (m-80) cc_final: 0.8498 (m-10) REVERT: B 124 TYR cc_start: 0.8045 (m-80) cc_final: 0.7440 (m-80) REVERT: B 175 GLN cc_start: 0.8456 (mm110) cc_final: 0.7939 (mp10) REVERT: B 214 ARG cc_start: 0.8109 (mtm180) cc_final: 0.7788 (mtm180) REVERT: B 228 ASP cc_start: 0.8196 (m-30) cc_final: 0.7895 (m-30) REVERT: D 59 ASN cc_start: 0.7088 (OUTLIER) cc_final: 0.6570 (t0) REVERT: E 31 ASN cc_start: 0.7912 (m-40) cc_final: 0.7502 (m110) outliers start: 27 outliers final: 22 residues processed: 149 average time/residue: 0.0958 time to fit residues: 19.5184 Evaluate side-chains 148 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 283 CYS Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 0.9980 chunk 89 optimal weight: 0.0770 chunk 76 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.2980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.174996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.137270 restraints weight = 15783.216| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.14 r_work: 0.3558 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8383 Z= 0.113 Angle : 0.538 10.735 11362 Z= 0.278 Chirality : 0.042 0.135 1275 Planarity : 0.003 0.035 1441 Dihedral : 4.837 39.196 1146 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.84 % Allowed : 19.21 % Favored : 76.95 % 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 are not related in a simple way. whole: 1.13 (0.26), residues: 1023 helix: 2.26 (0.25), residues: 416 sheet: -0.03 (0.33), residues: 219 loop : -0.39 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.010 0.001 TYR E 32 PHE 0.011 0.001 PHE B 199 TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8380) covalent geometry : angle 0.53806 (11356) SS BOND : bond 0.00211 ( 3) SS BOND : angle 0.67783 ( 6) hydrogen bonds : bond 0.04264 ( 453) hydrogen bonds : angle 4.44521 ( 1281) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 163 TRP cc_start: 0.8042 (m-10) cc_final: 0.7775 (m-10) REVERT: F 333 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7417 (m-10) REVERT: A 20 ARG cc_start: 0.7950 (ttm110) cc_final: 0.7608 (mtm110) REVERT: A 211 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7949 (mttm) REVERT: A 281 TRP cc_start: 0.8722 (m100) cc_final: 0.8458 (m100) REVERT: B 111 TYR cc_start: 0.8713 (m-80) cc_final: 0.8477 (m-10) REVERT: B 124 TYR cc_start: 0.8230 (m-80) cc_final: 0.7561 (m-80) REVERT: B 175 GLN cc_start: 0.8450 (mm110) cc_final: 0.7948 (mp10) REVERT: B 214 ARG cc_start: 0.8015 (mtm180) cc_final: 0.7724 (mtm180) REVERT: B 217 MET cc_start: 0.7444 (tpp) cc_final: 0.7179 (tpp) REVERT: B 228 ASP cc_start: 0.8122 (m-30) cc_final: 0.7760 (m-30) REVERT: B 264 TYR cc_start: 0.8174 (m-80) cc_final: 0.7324 (m-80) REVERT: D 59 ASN cc_start: 0.7053 (OUTLIER) cc_final: 0.6753 (t0) REVERT: E 29 PHE cc_start: 0.8514 (t80) cc_final: 0.7886 (t80) REVERT: E 31 ASN cc_start: 0.7814 (m-40) cc_final: 0.7433 (m110) outliers start: 33 outliers final: 25 residues processed: 155 average time/residue: 0.0919 time to fit residues: 19.7273 Evaluate side-chains 157 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 283 CYS Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 52 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.175036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.131989 restraints weight = 32428.002| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 4.75 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8383 Z= 0.118 Angle : 0.540 10.841 11362 Z= 0.280 Chirality : 0.042 0.231 1275 Planarity : 0.003 0.034 1441 Dihedral : 4.773 39.052 1146 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.62 % Allowed : 19.66 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.26), residues: 1023 helix: 2.25 (0.25), residues: 415 sheet: -0.01 (0.32), residues: 229 loop : -0.35 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 317 TYR 0.011 0.001 TYR E 32 PHE 0.011 0.001 PHE F 333 TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8380) covalent geometry : angle 0.53947 (11356) SS BOND : bond 0.00213 ( 3) SS BOND : angle 0.69544 ( 6) hydrogen bonds : bond 0.04280 ( 453) hydrogen bonds : angle 4.44546 ( 1281) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 163 TRP cc_start: 0.7754 (m-10) cc_final: 0.7502 (m-10) REVERT: F 333 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7565 (m-10) REVERT: A 20 ARG cc_start: 0.7839 (ttm110) cc_final: 0.7434 (mtm110) REVERT: A 211 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7739 (mttm) REVERT: A 281 TRP cc_start: 0.8701 (m100) cc_final: 0.8478 (m100) REVERT: B 111 TYR cc_start: 0.8672 (m-80) cc_final: 0.8444 (m-10) REVERT: B 124 TYR cc_start: 0.8171 (m-80) cc_final: 0.7626 (m-80) REVERT: B 175 GLN cc_start: 0.8337 (mm110) cc_final: 0.7813 (mp10) REVERT: B 214 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7574 (mtm180) REVERT: B 217 MET cc_start: 0.7524 (tpp) cc_final: 0.7244 (tpp) REVERT: B 228 ASP cc_start: 0.8141 (m-30) cc_final: 0.7871 (m-30) REVERT: B 264 TYR cc_start: 0.8064 (m-80) cc_final: 0.7404 (m-80) REVERT: E 29 PHE cc_start: 0.8637 (t80) cc_final: 0.7981 (t80) REVERT: E 31 ASN cc_start: 0.7724 (m-40) cc_final: 0.7329 (m110) outliers start: 31 outliers final: 25 residues processed: 151 average time/residue: 0.0897 time to fit residues: 18.7707 Evaluate side-chains 163 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 283 CYS Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 84 optimal weight: 30.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN D 59 ASN E 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.169984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.130454 restraints weight = 28241.876| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 5.08 r_work: 0.3369 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8383 Z= 0.170 Angle : 0.585 12.725 11362 Z= 0.305 Chirality : 0.044 0.230 1275 Planarity : 0.004 0.037 1441 Dihedral : 4.958 44.702 1146 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.52 % Allowed : 19.32 % Favored : 76.16 % 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 are not related in a simple way. whole: 1.05 (0.26), residues: 1023 helix: 2.12 (0.25), residues: 416 sheet: -0.04 (0.33), residues: 232 loop : -0.37 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 317 TYR 0.012 0.001 TYR E 32 PHE 0.014 0.001 PHE F 333 TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8380) covalent geometry : angle 0.58529 (11356) SS BOND : bond 0.00202 ( 3) SS BOND : angle 0.85041 ( 6) hydrogen bonds : bond 0.04765 ( 453) hydrogen bonds : angle 4.59817 ( 1281) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 163 TRP cc_start: 0.7953 (m-10) cc_final: 0.7705 (m-10) REVERT: F 311 ASN cc_start: 0.7493 (m-40) cc_final: 0.6869 (t0) REVERT: F 333 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7606 (m-10) REVERT: A 16 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8068 (mt-10) REVERT: A 20 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7704 (mtm110) REVERT: A 211 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7991 (mttm) REVERT: A 392 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8413 (mm-30) REVERT: B 111 TYR cc_start: 0.8890 (m-80) cc_final: 0.8659 (m-10) REVERT: B 175 GLN cc_start: 0.8419 (mm110) cc_final: 0.7934 (mp10) REVERT: B 217 MET cc_start: 0.7469 (tpp) cc_final: 0.7210 (tpp) REVERT: B 228 ASP cc_start: 0.8221 (m-30) cc_final: 0.7768 (m-30) REVERT: D 59 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.6896 (t0) REVERT: E 31 ASN cc_start: 0.7968 (m-40) cc_final: 0.7561 (m110) outliers start: 39 outliers final: 32 residues processed: 161 average time/residue: 0.0939 time to fit residues: 20.6430 Evaluate side-chains 171 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 283 CYS Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 65 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.173543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.135363 restraints weight = 22727.702| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 4.20 r_work: 0.3502 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8383 Z= 0.121 Angle : 0.556 11.860 11362 Z= 0.289 Chirality : 0.042 0.210 1275 Planarity : 0.003 0.035 1441 Dihedral : 4.856 42.072 1146 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.95 % Allowed : 19.89 % Favored : 76.16 % 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 are not related in a simple way. whole: 1.25 (0.27), residues: 1023 helix: 2.37 (0.25), residues: 410 sheet: -0.01 (0.33), residues: 230 loop : -0.28 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 317 TYR 0.011 0.001 TYR E 32 PHE 0.012 0.001 PHE B 199 TRP 0.033 0.001 TRP B 63 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8380) covalent geometry : angle 0.55587 (11356) SS BOND : bond 0.00202 ( 3) SS BOND : angle 0.69205 ( 6) hydrogen bonds : bond 0.04380 ( 453) hydrogen bonds : angle 4.48706 ( 1281) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 163 TRP cc_start: 0.7850 (m-10) cc_final: 0.7594 (m-10) REVERT: F 210 MET cc_start: 0.8160 (mtm) cc_final: 0.7939 (mtp) REVERT: F 297 PHE cc_start: 0.8419 (m-80) cc_final: 0.8212 (m-10) REVERT: F 311 ASN cc_start: 0.7367 (m-40) cc_final: 0.6753 (t0) REVERT: F 333 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7490 (m-10) REVERT: A 16 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8007 (mt-10) REVERT: A 20 ARG cc_start: 0.7970 (ttm110) cc_final: 0.7639 (mtm110) REVERT: A 49 ASP cc_start: 0.8251 (p0) cc_final: 0.8032 (p0) REVERT: A 211 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8024 (mttm) REVERT: A 281 TRP cc_start: 0.8807 (m100) cc_final: 0.8543 (m100) REVERT: A 392 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8315 (mm-30) REVERT: B 124 TYR cc_start: 0.8295 (m-80) cc_final: 0.7667 (m-80) REVERT: B 175 GLN cc_start: 0.8428 (mm110) cc_final: 0.7984 (mp10) REVERT: B 217 MET cc_start: 0.7451 (tpp) cc_final: 0.7196 (tpp) REVERT: B 228 ASP cc_start: 0.8281 (m-30) cc_final: 0.7847 (m-30) REVERT: B 253 PHE cc_start: 0.7990 (m-80) cc_final: 0.7711 (m-80) REVERT: B 264 TYR cc_start: 0.8165 (m-80) cc_final: 0.7615 (m-80) REVERT: D 59 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7021 (t0) outliers start: 34 outliers final: 31 residues processed: 160 average time/residue: 0.0931 time to fit residues: 20.4850 Evaluate side-chains 166 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 283 CYS Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.173631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134727 restraints weight = 31885.591| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 5.78 r_work: 0.3412 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8383 Z= 0.127 Angle : 0.557 11.778 11362 Z= 0.290 Chirality : 0.043 0.207 1275 Planarity : 0.003 0.035 1441 Dihedral : 4.800 39.269 1146 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.07 % Allowed : 20.23 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.27), residues: 1023 helix: 2.41 (0.25), residues: 409 sheet: -0.02 (0.33), residues: 237 loop : -0.25 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 317 TYR 0.011 0.001 TYR E 32 PHE 0.012 0.001 PHE B 199 TRP 0.045 0.001 TRP B 63 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8380) covalent geometry : angle 0.55711 (11356) SS BOND : bond 0.00201 ( 3) SS BOND : angle 0.72195 ( 6) hydrogen bonds : bond 0.04375 ( 453) hydrogen bonds : angle 4.47551 ( 1281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2292.43 seconds wall clock time: 39 minutes 56.00 seconds (2396.00 seconds total)