Starting phenix.real_space_refine on Wed Feb 12 12:01:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xof_38527/02_2025/8xof_38527.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xof_38527/02_2025/8xof_38527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xof_38527/02_2025/8xof_38527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xof_38527/02_2025/8xof_38527.map" model { file = "/net/cci-nas-00/data/ceres_data/8xof_38527/02_2025/8xof_38527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xof_38527/02_2025/8xof_38527.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 51 5.16 5 Cl 2 4.86 5 C 5094 2.51 5 N 1408 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8025 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1863 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2573 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 960 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2163 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain breaks: 2 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'A1LVW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.68, per 1000 atoms: 0.58 Number of scatterers: 8025 At special positions: 0 Unit cell: (83.95, 96.36, 126.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 51 16.00 O 1470 8.00 N 1408 7.00 C 5094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.37 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 886.2 milliseconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 43.3% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.627A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.690A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.507A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.279A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.621A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.634A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 51 through 87 removed outlier: 4.287A pdb=" N PHE R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 88 through 91 Processing helix chain 'R' and resid 92 through 117 removed outlier: 3.734A pdb=" N TYR R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE R 117 " --> pdb=" O LEU R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 161 Processing helix chain 'R' and resid 170 through 198 Proline residue: R 192 - end of helix removed outlier: 3.681A pdb=" N LEU R 198 " --> pdb=" O THR R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 246 removed outlier: 5.396A pdb=" N VAL R 225 " --> pdb=" O LEU R 221 " (cutoff:3.500A) Proline residue: R 226 - end of helix Processing helix chain 'R' and resid 250 through 283 Proline residue: R 274 - end of helix removed outlier: 3.606A pdb=" N HIS R 282 " --> pdb=" O PHE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 325 removed outlier: 3.815A pdb=" N SER R 317 " --> pdb=" O ALA R 313 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 328 through 342 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.694A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.618A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.674A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.120A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.456A 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: 3.588A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.085A 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: 3.512A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.632A 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: 6.624A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.652A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.996A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1725 1.33 - 1.45: 1881 1.45 - 1.57: 4506 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 8186 Sorted by residual: bond pdb=" C17 A1LVW R 401 " pdb=" N08 A1LVW R 401 " ideal model delta sigma weight residual 1.343 1.449 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C16 A1LVW R 401 " pdb=" N07 A1LVW R 401 " ideal model delta sigma weight residual 1.359 1.451 -0.092 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C17 A1LVW R 401 " pdb=" C19 A1LVW R 401 " ideal model delta sigma weight residual 1.439 1.355 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C16 A1LVW R 401 " pdb=" C18 A1LVW R 401 " ideal model delta sigma weight residual 1.436 1.355 0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C32 A1LVW R 401 " pdb="CL01 A1LVW R 401 " ideal model delta sigma weight residual 1.731 1.784 -0.053 2.00e-02 2.50e+03 7.07e+00 ... (remaining 8181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 10807 1.46 - 2.92: 204 2.92 - 4.38: 51 4.38 - 5.84: 16 5.84 - 7.31: 7 Bond angle restraints: 11085 Sorted by residual: angle pdb=" N ARG A 356 " pdb=" CA ARG A 356 " pdb=" CB ARG A 356 " ideal model delta sigma weight residual 110.40 116.39 -5.99 1.63e+00 3.76e-01 1.35e+01 angle pdb=" N ASN N 35 " pdb=" CA ASN N 35 " pdb=" C ASN N 35 " ideal model delta sigma weight residual 108.99 113.67 -4.68 1.57e+00 4.06e-01 8.88e+00 angle pdb=" N TYR B 105 " pdb=" CA TYR B 105 " pdb=" C TYR B 105 " ideal model delta sigma weight residual 108.90 104.14 4.76 1.63e+00 3.76e-01 8.52e+00 angle pdb=" N ASP R 111 " pdb=" CA ASP R 111 " pdb=" C ASP R 111 " ideal model delta sigma weight residual 112.54 109.12 3.42 1.22e+00 6.72e-01 7.86e+00 angle pdb=" N HIS R 302 " pdb=" CA HIS R 302 " pdb=" C HIS R 302 " ideal model delta sigma weight residual 109.81 115.81 -6.00 2.21e+00 2.05e-01 7.37e+00 ... (remaining 11080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4302 17.71 - 35.43: 415 35.43 - 53.14: 118 53.14 - 70.86: 24 70.86 - 88.57: 12 Dihedral angle restraints: 4871 sinusoidal: 1919 harmonic: 2952 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -125.77 39.77 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -157.81 -22.19 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 4868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1071 0.056 - 0.112: 150 0.112 - 0.169: 31 0.169 - 0.225: 3 0.225 - 0.281: 1 Chirality restraints: 1256 Sorted by residual: chirality pdb=" CA ARG A 356 " pdb=" N ARG A 356 " pdb=" C ARG A 356 " pdb=" CB ARG A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA TYR B 105 " pdb=" N TYR B 105 " pdb=" C TYR B 105 " pdb=" CB TYR B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE R 308 " pdb=" CA ILE R 308 " pdb=" CG1 ILE R 308 " pdb=" CG2 ILE R 308 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1253 not shown) Planarity restraints: 1411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 197 " -0.202 9.50e-02 1.11e+02 9.09e-02 5.63e+00 pdb=" NE ARG B 197 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 197 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 197 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 197 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 214 " -0.130 9.50e-02 1.11e+02 5.85e-02 2.42e+00 pdb=" NE ARG B 214 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 214 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 214 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 214 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 282 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C LEU A 282 " 0.025 2.00e-02 2.50e+03 pdb=" O LEU A 282 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG A 283 " -0.009 2.00e-02 2.50e+03 ... (remaining 1408 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 250 2.71 - 3.26: 8166 3.26 - 3.80: 13118 3.80 - 4.35: 17277 4.35 - 4.90: 29059 Nonbonded interactions: 67870 Sorted by model distance: nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.160 3.040 nonbonded pdb=" OG1 THR R 92 " pdb=" OD2 ASP R 95 " model vdw 2.204 3.040 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.260 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.262 3.040 nonbonded pdb=" OE1 GLN A 59 " pdb=" ND2 ASN A 371 " model vdw 2.297 3.120 ... (remaining 67865 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.640 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 8186 Z= 0.246 Angle : 0.578 7.305 11085 Z= 0.308 Chirality : 0.042 0.281 1256 Planarity : 0.004 0.091 1411 Dihedral : 15.971 88.571 2952 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.46 % Allowed : 16.88 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.28), residues: 997 helix: 2.91 (0.26), residues: 385 sheet: -0.40 (0.32), residues: 221 loop : 0.19 (0.34), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.007 0.001 HIS R 245 PHE 0.009 0.001 PHE A 212 TYR 0.019 0.001 TYR R 55 ARG 0.013 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 145 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 358 ILE cc_start: 0.9182 (mm) cc_final: 0.8957 (mm) REVERT: B 16 ASN cc_start: 0.8032 (m-40) cc_final: 0.7756 (m-40) REVERT: B 17 GLN cc_start: 0.7900 (tt0) cc_final: 0.7431 (mt0) REVERT: B 44 GLN cc_start: 0.8162 (tt0) cc_final: 0.7813 (tt0) REVERT: B 262 MET cc_start: 0.8897 (tpt) cc_final: 0.8658 (tpp) outliers start: 4 outliers final: 2 residues processed: 146 average time/residue: 1.3146 time to fit residues: 202.7517 Evaluate side-chains 135 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.5980 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 88 optimal weight: 0.0170 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.156647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115381 restraints weight = 10083.034| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.46 r_work: 0.3364 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8186 Z= 0.203 Angle : 0.553 10.293 11085 Z= 0.293 Chirality : 0.043 0.159 1256 Planarity : 0.004 0.040 1411 Dihedral : 5.891 75.442 1114 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.82 % Allowed : 15.72 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.27), residues: 997 helix: 2.82 (0.25), residues: 390 sheet: -0.41 (0.33), residues: 208 loop : 0.20 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.009 0.001 HIS R 245 PHE 0.014 0.001 PHE A 212 TYR 0.017 0.001 TYR R 55 ARG 0.011 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7959 (mm-30) REVERT: A 358 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8862 (mm) REVERT: B 16 ASN cc_start: 0.7976 (m-40) cc_final: 0.7669 (m-40) REVERT: B 46 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7182 (mtm-85) REVERT: B 153 ASP cc_start: 0.8118 (m-30) cc_final: 0.7778 (p0) REVERT: B 214 ARG cc_start: 0.8646 (mmm160) cc_final: 0.8375 (mmm-85) REVERT: B 261 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8512 (mp) REVERT: B 262 MET cc_start: 0.9033 (tpt) cc_final: 0.8707 (tpp) REVERT: N 120 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8439 (mp10) REVERT: R 95 ASP cc_start: 0.8779 (m-30) cc_final: 0.8539 (m-30) outliers start: 33 outliers final: 10 residues processed: 160 average time/residue: 1.1585 time to fit residues: 197.0907 Evaluate side-chains 144 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 170 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 68 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 71 optimal weight: 0.0980 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.154070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112059 restraints weight = 10248.465| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.48 r_work: 0.3308 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8186 Z= 0.341 Angle : 0.594 11.412 11085 Z= 0.312 Chirality : 0.045 0.243 1256 Planarity : 0.004 0.044 1411 Dihedral : 5.993 72.417 1114 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.86 % Allowed : 14.91 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.27), residues: 997 helix: 2.64 (0.26), residues: 390 sheet: -0.47 (0.32), residues: 225 loop : 0.09 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.008 0.001 HIS R 245 PHE 0.017 0.002 PHE B 292 TYR 0.020 0.002 TYR R 55 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8970 (mm) REVERT: B 46 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7357 (mtm-85) REVERT: B 153 ASP cc_start: 0.8173 (m-30) cc_final: 0.7813 (p0) REVERT: B 214 ARG cc_start: 0.8631 (mmm160) cc_final: 0.8346 (mmm-85) REVERT: B 261 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8603 (mp) REVERT: B 262 MET cc_start: 0.9014 (tpt) cc_final: 0.8696 (tpp) REVERT: B 292 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8129 (p90) REVERT: N 120 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8450 (mp10) REVERT: R 99 ILE cc_start: 0.8392 (pt) cc_final: 0.8172 (pp) outliers start: 42 outliers final: 16 residues processed: 152 average time/residue: 1.1834 time to fit residues: 191.6964 Evaluate side-chains 141 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 329 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.0020 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.156895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115474 restraints weight = 10177.567| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.48 r_work: 0.3362 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8186 Z= 0.175 Angle : 0.527 10.739 11085 Z= 0.276 Chirality : 0.042 0.207 1256 Planarity : 0.004 0.045 1411 Dihedral : 5.754 75.504 1114 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.35 % Allowed : 17.11 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.27), residues: 997 helix: 2.69 (0.26), residues: 390 sheet: -0.25 (0.33), residues: 220 loop : 0.04 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.008 0.001 HIS R 245 PHE 0.013 0.001 PHE A 212 TYR 0.018 0.001 TYR R 55 ARG 0.008 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8856 (mm) REVERT: B 16 ASN cc_start: 0.8094 (m-40) cc_final: 0.7653 (m-40) REVERT: B 42 ARG cc_start: 0.7574 (ttt-90) cc_final: 0.6937 (ttt-90) REVERT: B 44 GLN cc_start: 0.8310 (tt0) cc_final: 0.7781 (tt0) REVERT: B 46 ARG cc_start: 0.7902 (mtt180) cc_final: 0.7384 (mtm-85) REVERT: B 153 ASP cc_start: 0.8173 (m-30) cc_final: 0.7844 (p0) REVERT: B 214 ARG cc_start: 0.8630 (mmm160) cc_final: 0.8359 (mmm-85) REVERT: B 261 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8595 (mp) REVERT: N 120 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8411 (mp10) REVERT: R 99 ILE cc_start: 0.8403 (pt) cc_final: 0.8177 (pp) outliers start: 29 outliers final: 12 residues processed: 148 average time/residue: 1.2152 time to fit residues: 191.0146 Evaluate side-chains 140 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 329 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 86 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.157422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115943 restraints weight = 10043.307| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.46 r_work: 0.3368 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8186 Z= 0.181 Angle : 0.526 11.137 11085 Z= 0.273 Chirality : 0.042 0.214 1256 Planarity : 0.004 0.045 1411 Dihedral : 5.636 75.748 1114 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.70 % Allowed : 17.46 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.27), residues: 997 helix: 2.71 (0.26), residues: 391 sheet: -0.22 (0.32), residues: 230 loop : 0.03 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.008 0.001 HIS R 245 PHE 0.015 0.001 PHE R 70 TYR 0.022 0.001 TYR N 60 ARG 0.010 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6898 (mptp) cc_final: 0.6628 (mptt) REVERT: A 391 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.7826 (t80) REVERT: B 16 ASN cc_start: 0.8150 (m-40) cc_final: 0.7771 (m-40) REVERT: B 46 ARG cc_start: 0.7920 (mtt180) cc_final: 0.7400 (mtm-85) REVERT: B 153 ASP cc_start: 0.8179 (m-30) cc_final: 0.7864 (p0) REVERT: B 214 ARG cc_start: 0.8637 (mmm160) cc_final: 0.8373 (mmm-85) REVERT: B 261 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8607 (mp) REVERT: N 80 TYR cc_start: 0.8363 (m-80) cc_final: 0.8121 (m-80) REVERT: N 120 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8408 (mp10) REVERT: R 88 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.6052 (ttt180) REVERT: R 95 ASP cc_start: 0.8922 (m-30) cc_final: 0.8712 (m-30) REVERT: R 99 ILE cc_start: 0.8409 (pt) cc_final: 0.8188 (pp) REVERT: R 135 LEU cc_start: 0.8440 (mm) cc_final: 0.8238 (mp) outliers start: 32 outliers final: 16 residues processed: 147 average time/residue: 1.2007 time to fit residues: 187.5007 Evaluate side-chains 143 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 170 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 83 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.158152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116952 restraints weight = 10035.664| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.44 r_work: 0.3393 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8186 Z= 0.168 Angle : 0.520 9.934 11085 Z= 0.270 Chirality : 0.042 0.269 1256 Planarity : 0.003 0.045 1411 Dihedral : 5.555 76.235 1114 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.58 % Allowed : 18.03 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.27), residues: 997 helix: 2.77 (0.26), residues: 391 sheet: -0.19 (0.32), residues: 230 loop : 0.04 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS R 245 PHE 0.014 0.001 PHE A 212 TYR 0.014 0.001 TYR R 156 ARG 0.008 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: A 391 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7813 (t80) REVERT: B 16 ASN cc_start: 0.8128 (m-40) cc_final: 0.7733 (m-40) REVERT: B 46 ARG cc_start: 0.7923 (mtt180) cc_final: 0.7386 (mtm-85) REVERT: B 153 ASP cc_start: 0.8176 (m-30) cc_final: 0.7860 (p0) REVERT: B 175 GLN cc_start: 0.7813 (mm110) cc_final: 0.7608 (mm110) REVERT: B 214 ARG cc_start: 0.8622 (mmm160) cc_final: 0.8356 (mmm-85) REVERT: B 261 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8601 (mp) REVERT: N 80 TYR cc_start: 0.8329 (m-80) cc_final: 0.7972 (m-80) REVERT: N 120 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8394 (mp10) REVERT: R 88 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.6063 (ttt180) REVERT: R 95 ASP cc_start: 0.8895 (m-30) cc_final: 0.8664 (m-30) REVERT: R 99 ILE cc_start: 0.8386 (pt) cc_final: 0.8164 (pp) REVERT: R 216 TRP cc_start: 0.7887 (OUTLIER) cc_final: 0.7274 (m100) outliers start: 31 outliers final: 14 residues processed: 150 average time/residue: 1.2411 time to fit residues: 198.2437 Evaluate side-chains 146 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 216 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.156762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115167 restraints weight = 10197.501| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.48 r_work: 0.3354 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8186 Z= 0.227 Angle : 0.556 11.932 11085 Z= 0.286 Chirality : 0.043 0.331 1256 Planarity : 0.004 0.045 1411 Dihedral : 5.606 75.415 1114 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.35 % Allowed : 19.31 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.27), residues: 997 helix: 2.72 (0.26), residues: 391 sheet: -0.23 (0.32), residues: 232 loop : 0.05 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.007 0.001 HIS R 245 PHE 0.013 0.001 PHE A 212 TYR 0.023 0.002 TYR N 60 ARG 0.008 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: B 16 ASN cc_start: 0.8186 (m-40) cc_final: 0.7758 (m-40) REVERT: B 42 ARG cc_start: 0.7382 (ttt-90) cc_final: 0.6769 (ttp80) REVERT: B 44 GLN cc_start: 0.7972 (tt0) cc_final: 0.7683 (tt0) REVERT: B 46 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7454 (mtm-85) REVERT: B 153 ASP cc_start: 0.8167 (m-30) cc_final: 0.7859 (p0) REVERT: B 214 ARG cc_start: 0.8632 (mmm160) cc_final: 0.8366 (mmm-85) REVERT: B 261 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8603 (mp) REVERT: N 80 TYR cc_start: 0.8397 (m-80) cc_final: 0.8176 (m-80) REVERT: N 120 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8441 (mp10) REVERT: R 88 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.6207 (ttt180) REVERT: R 95 ASP cc_start: 0.8914 (m-30) cc_final: 0.8670 (m-30) REVERT: R 99 ILE cc_start: 0.8413 (pt) cc_final: 0.8184 (pp) REVERT: R 326 PHE cc_start: 0.8452 (m-10) cc_final: 0.8231 (m-10) outliers start: 29 outliers final: 19 residues processed: 141 average time/residue: 1.2202 time to fit residues: 182.6174 Evaluate side-chains 144 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 170 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.157692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.116140 restraints weight = 10207.849| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.50 r_work: 0.3371 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8186 Z= 0.185 Angle : 0.564 15.997 11085 Z= 0.285 Chirality : 0.043 0.239 1256 Planarity : 0.003 0.046 1411 Dihedral : 5.529 74.769 1114 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.35 % Allowed : 19.65 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.27), residues: 997 helix: 2.67 (0.26), residues: 391 sheet: -0.18 (0.32), residues: 232 loop : 0.06 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.008 0.001 HIS R 245 PHE 0.013 0.001 PHE A 212 TYR 0.026 0.001 TYR N 60 ARG 0.009 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7935 (pm20) REVERT: A 386 MET cc_start: 0.8099 (mtm) cc_final: 0.7736 (ttm) REVERT: B 16 ASN cc_start: 0.8169 (m-40) cc_final: 0.7736 (m-40) REVERT: B 46 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7476 (mtm-85) REVERT: B 153 ASP cc_start: 0.8174 (m-30) cc_final: 0.7867 (p0) REVERT: B 214 ARG cc_start: 0.8628 (mmm160) cc_final: 0.8358 (mmm-85) REVERT: B 261 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8582 (mp) REVERT: G 21 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6961 (ttt) REVERT: N 80 TYR cc_start: 0.8370 (m-80) cc_final: 0.8030 (m-80) REVERT: N 120 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8408 (mp10) REVERT: R 88 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.6237 (ttt180) REVERT: R 95 ASP cc_start: 0.8901 (m-30) cc_final: 0.8666 (m-30) REVERT: R 99 ILE cc_start: 0.8400 (pt) cc_final: 0.8177 (pp) REVERT: R 326 PHE cc_start: 0.8441 (m-10) cc_final: 0.8188 (m-10) outliers start: 29 outliers final: 23 residues processed: 146 average time/residue: 1.1894 time to fit residues: 184.4183 Evaluate side-chains 154 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 170 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 96 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 85 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.158162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.116634 restraints weight = 10278.941| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.50 r_work: 0.3382 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8186 Z= 0.174 Angle : 0.540 11.329 11085 Z= 0.280 Chirality : 0.042 0.254 1256 Planarity : 0.004 0.046 1411 Dihedral : 5.500 75.499 1114 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.35 % Allowed : 20.23 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.27), residues: 997 helix: 2.72 (0.26), residues: 388 sheet: -0.20 (0.32), residues: 232 loop : -0.01 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.008 0.001 HIS R 245 PHE 0.013 0.001 PHE A 212 TYR 0.026 0.001 TYR N 60 ARG 0.009 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6922 (mptp) cc_final: 0.6689 (mptt) REVERT: A 370 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7945 (pm20) REVERT: A 386 MET cc_start: 0.8079 (mtm) cc_final: 0.7729 (ttm) REVERT: B 16 ASN cc_start: 0.8139 (m-40) cc_final: 0.7723 (m-40) REVERT: B 44 GLN cc_start: 0.7947 (tt0) cc_final: 0.7507 (pt0) REVERT: B 46 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7471 (mtm-85) REVERT: B 153 ASP cc_start: 0.8173 (m-30) cc_final: 0.7868 (p0) REVERT: B 214 ARG cc_start: 0.8611 (mmm160) cc_final: 0.8344 (mmm-85) REVERT: B 261 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8573 (mp) REVERT: N 80 TYR cc_start: 0.8362 (m-80) cc_final: 0.8028 (m-80) REVERT: N 120 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8407 (mp10) REVERT: R 88 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.6193 (ttt180) REVERT: R 95 ASP cc_start: 0.8895 (m-30) cc_final: 0.8676 (m-30) REVERT: R 99 ILE cc_start: 0.8402 (pt) cc_final: 0.8179 (pp) REVERT: R 326 PHE cc_start: 0.8444 (m-10) cc_final: 0.8196 (m-10) outliers start: 29 outliers final: 21 residues processed: 145 average time/residue: 1.1630 time to fit residues: 179.3664 Evaluate side-chains 151 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 170 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.156462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.114627 restraints weight = 10094.603| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.48 r_work: 0.3352 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8186 Z= 0.241 Angle : 0.577 11.694 11085 Z= 0.297 Chirality : 0.044 0.241 1256 Planarity : 0.004 0.045 1411 Dihedral : 5.605 74.114 1114 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.35 % Allowed : 20.58 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.27), residues: 997 helix: 2.66 (0.26), residues: 388 sheet: -0.29 (0.32), residues: 232 loop : -0.04 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.008 0.001 HIS R 245 PHE 0.014 0.001 PHE A 212 TYR 0.019 0.002 TYR R 156 ARG 0.009 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7872 (mttp) cc_final: 0.7568 (ttmm) REVERT: A 370 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7968 (pm20) REVERT: A 386 MET cc_start: 0.8137 (mtm) cc_final: 0.7785 (ttm) REVERT: B 42 ARG cc_start: 0.7382 (ttt-90) cc_final: 0.7073 (ttt-90) REVERT: B 44 GLN cc_start: 0.7799 (tt0) cc_final: 0.7439 (pt0) REVERT: B 46 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7478 (mtm-85) REVERT: B 153 ASP cc_start: 0.8180 (m-30) cc_final: 0.7861 (p0) REVERT: B 214 ARG cc_start: 0.8617 (mmm160) cc_final: 0.8352 (mmm-85) REVERT: B 261 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8582 (mp) REVERT: N 80 TYR cc_start: 0.8413 (m-80) cc_final: 0.8079 (m-80) REVERT: N 120 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8402 (mp10) REVERT: R 88 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.6327 (ttt180) REVERT: R 95 ASP cc_start: 0.8904 (m-30) cc_final: 0.8660 (m-30) REVERT: R 99 ILE cc_start: 0.8428 (pt) cc_final: 0.8201 (pp) REVERT: R 114 ILE cc_start: 0.6490 (OUTLIER) cc_final: 0.6228 (pt) REVERT: R 326 PHE cc_start: 0.8463 (m-10) cc_final: 0.8208 (m-10) outliers start: 29 outliers final: 19 residues processed: 140 average time/residue: 1.2237 time to fit residues: 181.9807 Evaluate side-chains 148 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 170 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 51 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.158422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116878 restraints weight = 10150.625| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.48 r_work: 0.3391 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8186 Z= 0.169 Angle : 0.539 11.337 11085 Z= 0.279 Chirality : 0.042 0.241 1256 Planarity : 0.004 0.045 1411 Dihedral : 5.473 75.555 1114 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.89 % Allowed : 21.16 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.27), residues: 997 helix: 2.71 (0.25), residues: 388 sheet: -0.29 (0.32), residues: 235 loop : -0.01 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.008 0.001 HIS R 245 PHE 0.013 0.001 PHE A 212 TYR 0.017 0.001 TYR R 156 ARG 0.009 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 7302.44 seconds wall clock time: 128 minutes 45.65 seconds (7725.65 seconds total)