Starting phenix.real_space_refine on Wed Sep 17 09:51:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xof_38527/09_2025/8xof_38527.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xof_38527/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xof_38527/09_2025/8xof_38527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xof_38527/09_2025/8xof_38527.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xof_38527/09_2025/8xof_38527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xof_38527/09_2025/8xof_38527.map" } resolution = 2.6 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= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.15, per 1000 atoms: 0.27 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: 0.69 Conformation dependent library (CDL) restraints added in 468.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.28 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: 1.30 Time building geometry restraints manager: 0.93 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.380 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.300 ------------------------------------------------------------------------------- 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 : 0.005 0.335 8187 Z= 0.276 Angle : 0.622 19.691 11087 Z= 0.327 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (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 ARG 0.013 0.000 ARG B 197 TYR 0.019 0.001 TYR R 55 PHE 0.009 0.001 PHE A 212 TRP 0.016 0.001 TRP B 82 HIS 0.007 0.001 HIS R 245 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8186) covalent geometry : angle 0.57799 (11085) SS BOND : bond 0.33470 ( 1) SS BOND : angle 17.13625 ( 2) hydrogen bonds : bond 0.13664 ( 440) hydrogen bonds : angle 5.46106 ( 1257) *********************** 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 : 0.314 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: 0.8657 (tpp) outliers start: 4 outliers final: 2 residues processed: 146 average time/residue: 0.6562 time to fit residues: 100.9267 Evaluate side-chains 134 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.156817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115455 restraints weight = 10113.502| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.47 r_work: 0.3369 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8187 Z= 0.136 Angle : 0.549 10.239 11087 Z= 0.292 Chirality : 0.043 0.160 1256 Planarity : 0.004 0.040 1411 Dihedral : 5.858 74.749 1114 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.82 % Allowed : 15.49 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.27), residues: 997 helix: 2.81 (0.25), residues: 388 sheet: -0.40 (0.33), residues: 208 loop : 0.19 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 96 TYR 0.017 0.001 TYR R 55 PHE 0.014 0.001 PHE A 212 TRP 0.016 0.001 TRP B 82 HIS 0.009 0.001 HIS R 245 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8186) covalent geometry : angle 0.54870 (11085) SS BOND : bond 0.00136 ( 1) SS BOND : angle 2.19997 ( 2) hydrogen bonds : bond 0.04389 ( 440) hydrogen bonds : angle 4.63844 ( 1257) *********************** 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 175 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8037 (mm-30) REVERT: A 358 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8838 (mm) REVERT: B 16 ASN cc_start: 0.7996 (m-40) cc_final: 0.7688 (m-40) REVERT: B 42 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.7052 (ttt-90) REVERT: B 46 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7153 (mtm-85) REVERT: B 153 ASP cc_start: 0.8122 (m-30) cc_final: 0.7767 (p0) REVERT: B 214 ARG cc_start: 0.8619 (mmm160) cc_final: 0.8349 (mmm-85) REVERT: B 261 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8529 (mp) REVERT: B 262 MET cc_start: 0.9023 (tpt) cc_final: 0.8694 (tpp) REVERT: N 120 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8426 (mp10) REVERT: R 95 ASP cc_start: 0.8757 (m-30) cc_final: 0.8529 (m-30) outliers start: 33 outliers final: 9 residues processed: 158 average time/residue: 0.5694 time to fit residues: 95.4896 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 : 0.277 ------------------------------------------------------------------------------- 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 42 ARG 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 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 28 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.156595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115029 restraints weight = 10041.961| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.47 r_work: 0.3357 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8187 Z= 0.140 Angle : 0.539 10.736 11087 Z= 0.282 Chirality : 0.043 0.235 1256 Planarity : 0.004 0.042 1411 Dihedral : 5.761 74.522 1114 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.82 % Allowed : 16.42 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.27), residues: 997 helix: 2.77 (0.26), residues: 390 sheet: -0.31 (0.33), residues: 222 loop : 0.21 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.019 0.002 TYR R 55 PHE 0.014 0.001 PHE A 212 TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS R 245 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8186) covalent geometry : angle 0.53785 (11085) SS BOND : bond 0.00140 ( 1) SS BOND : angle 2.04446 ( 2) hydrogen bonds : bond 0.04167 ( 440) hydrogen bonds : angle 4.46700 ( 1257) *********************** 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 168 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6844 (mptp) cc_final: 0.6490 (mptt) REVERT: A 27 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7966 (mm-30) REVERT: A 358 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8890 (mm) REVERT: A 391 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7976 (t80) REVERT: B 44 GLN cc_start: 0.8362 (tt0) cc_final: 0.8012 (tt0) REVERT: B 46 ARG cc_start: 0.7816 (mtt180) cc_final: 0.7317 (mtm-85) REVERT: B 153 ASP cc_start: 0.8186 (m-30) cc_final: 0.7833 (p0) REVERT: B 214 ARG cc_start: 0.8622 (mmm160) cc_final: 0.8351 (mmm-85) REVERT: B 261 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8590 (mp) REVERT: N 120 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8419 (mp10) REVERT: R 99 ILE cc_start: 0.8391 (pt) cc_final: 0.8177 (pp) outliers start: 33 outliers final: 10 residues processed: 151 average time/residue: 0.5559 time to fit residues: 89.1929 Evaluate side-chains 139 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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 62 SER Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 170 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.2980 chunk 24 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.154862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113014 restraints weight = 10338.641| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.49 r_work: 0.3326 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8187 Z= 0.199 Angle : 0.577 11.519 11087 Z= 0.301 Chirality : 0.044 0.230 1256 Planarity : 0.004 0.045 1411 Dihedral : 5.867 73.594 1114 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.28 % Allowed : 16.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.27), residues: 997 helix: 2.64 (0.26), residues: 390 sheet: -0.45 (0.32), residues: 226 loop : 0.13 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.019 0.002 TYR N 60 PHE 0.015 0.002 PHE A 212 TRP 0.016 0.002 TRP B 82 HIS 0.008 0.001 HIS R 245 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 8186) covalent geometry : angle 0.57694 (11085) SS BOND : bond 0.00061 ( 1) SS BOND : angle 1.82321 ( 2) hydrogen bonds : bond 0.04390 ( 440) hydrogen bonds : angle 4.53777 ( 1257) *********************** 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 163 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8920 (mm) REVERT: B 16 ASN cc_start: 0.8086 (m-40) cc_final: 0.7633 (m-40) REVERT: B 46 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7378 (mtm-85) REVERT: B 153 ASP cc_start: 0.8185 (m-30) cc_final: 0.7832 (p0) REVERT: B 214 ARG cc_start: 0.8620 (mmm160) cc_final: 0.8337 (mmm-85) REVERT: B 261 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8629 (mp) REVERT: N 120 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8437 (mp10) REVERT: R 99 ILE cc_start: 0.8426 (pt) cc_final: 0.8200 (pp) outliers start: 37 outliers final: 17 residues processed: 144 average time/residue: 0.5709 time to fit residues: 87.1630 Evaluate side-chains 142 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 57 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 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 = 0.3954 r_free = 0.3954 target = 0.156857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115393 restraints weight = 10139.621| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.48 r_work: 0.3362 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8187 Z= 0.122 Angle : 0.536 11.012 11087 Z= 0.281 Chirality : 0.043 0.264 1256 Planarity : 0.004 0.046 1411 Dihedral : 5.724 75.335 1114 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.58 % Allowed : 17.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.27), residues: 997 helix: 2.64 (0.26), residues: 391 sheet: -0.24 (0.32), residues: 230 loop : 0.08 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.020 0.001 TYR N 60 PHE 0.016 0.001 PHE R 70 TRP 0.017 0.001 TRP B 82 HIS 0.008 0.001 HIS R 245 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8186) covalent geometry : angle 0.53583 (11085) SS BOND : bond 0.00092 ( 1) SS BOND : angle 1.75638 ( 2) hydrogen bonds : bond 0.03907 ( 440) hydrogen bonds : angle 4.41074 ( 1257) *********************** 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 159 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8242 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 358 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8869 (mm) REVERT: B 16 ASN cc_start: 0.8118 (m-40) cc_final: 0.7713 (m-40) REVERT: B 42 ARG cc_start: 0.7448 (ttt-90) cc_final: 0.7135 (ttt-90) REVERT: B 46 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7401 (mtm-85) REVERT: B 153 ASP cc_start: 0.8181 (m-30) cc_final: 0.7847 (p0) REVERT: B 214 ARG cc_start: 0.8615 (mmm160) cc_final: 0.8345 (mmm-85) REVERT: B 261 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8601 (mp) REVERT: N 80 TYR cc_start: 0.8384 (m-80) cc_final: 0.8055 (m-80) REVERT: N 120 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8404 (mp10) REVERT: R 99 ILE cc_start: 0.8373 (pt) cc_final: 0.8154 (pp) REVERT: R 135 LEU cc_start: 0.8440 (mm) cc_final: 0.8230 (mp) outliers start: 31 outliers final: 18 residues processed: 146 average time/residue: 0.6159 time to fit residues: 95.5076 Evaluate side-chains 142 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 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 108 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 329 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.0070 chunk 5 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 0.1980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.158737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.117512 restraints weight = 10142.844| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.49 r_work: 0.3389 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8187 Z= 0.111 Angle : 0.524 11.024 11087 Z= 0.272 Chirality : 0.042 0.323 1256 Planarity : 0.003 0.045 1411 Dihedral : 5.557 76.265 1114 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.27), residues: 997 helix: 2.71 (0.26), residues: 391 sheet: -0.18 (0.33), residues: 230 loop : 0.08 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.024 0.001 TYR N 60 PHE 0.013 0.001 PHE A 212 TRP 0.017 0.001 TRP B 82 HIS 0.008 0.001 HIS R 245 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8186) covalent geometry : angle 0.52402 (11085) SS BOND : bond 0.00019 ( 1) SS BOND : angle 1.64518 ( 2) hydrogen bonds : bond 0.03707 ( 440) hydrogen bonds : angle 4.25734 ( 1257) *********************** 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 166 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6890 (mptp) cc_final: 0.6677 (mptt) REVERT: A 391 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.7809 (t80) REVERT: B 16 ASN cc_start: 0.8124 (m-40) cc_final: 0.7723 (m-40) REVERT: B 46 ARG cc_start: 0.7935 (mtt180) cc_final: 0.7413 (mtm-85) REVERT: B 153 ASP cc_start: 0.8186 (m-30) cc_final: 0.7873 (p0) REVERT: B 175 GLN cc_start: 0.7870 (mm110) cc_final: 0.7626 (mm110) REVERT: B 214 ARG cc_start: 0.8617 (mmm160) cc_final: 0.8347 (mmm-85) REVERT: B 261 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8569 (mp) REVERT: N 80 TYR cc_start: 0.8362 (m-80) cc_final: 0.7979 (m-80) REVERT: N 120 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8396 (mp10) REVERT: R 88 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.6074 (ttt180) REVERT: R 99 ILE cc_start: 0.8402 (pt) cc_final: 0.8181 (pp) REVERT: R 216 TRP cc_start: 0.7881 (OUTLIER) cc_final: 0.7276 (m100) outliers start: 31 outliers final: 15 residues processed: 154 average time/residue: 0.5990 time to fit residues: 97.6180 Evaluate side-chains 147 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 84 optimal weight: 10.0000 chunk 88 optimal weight: 0.0000 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.159218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.117976 restraints weight = 10188.100| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.49 r_work: 0.3398 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8187 Z= 0.111 Angle : 0.523 10.151 11087 Z= 0.271 Chirality : 0.042 0.233 1256 Planarity : 0.003 0.044 1411 Dihedral : 5.475 75.344 1114 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.89 % Allowed : 19.19 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.27), residues: 997 helix: 2.76 (0.26), residues: 391 sheet: -0.15 (0.33), residues: 233 loop : 0.07 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.014 0.001 TYR R 156 PHE 0.013 0.001 PHE A 212 TRP 0.012 0.001 TRP A 234 HIS 0.008 0.001 HIS R 245 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8186) covalent geometry : angle 0.52262 (11085) SS BOND : bond 0.00037 ( 1) SS BOND : angle 1.53063 ( 2) hydrogen bonds : bond 0.03671 ( 440) hydrogen bonds : angle 4.19506 ( 1257) *********************** 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 158 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6891 (mptp) cc_final: 0.6680 (mptt) REVERT: A 370 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: A 386 MET cc_start: 0.8092 (mtm) cc_final: 0.7711 (ttm) REVERT: A 391 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7817 (t80) REVERT: B 16 ASN cc_start: 0.8164 (m-40) cc_final: 0.7745 (m-40) REVERT: B 42 ARG cc_start: 0.7497 (ttt-90) cc_final: 0.7077 (ttp80) REVERT: B 46 ARG cc_start: 0.7974 (mtt180) cc_final: 0.7435 (mtm-85) REVERT: B 153 ASP cc_start: 0.8170 (m-30) cc_final: 0.7873 (p0) REVERT: B 175 GLN cc_start: 0.7871 (mm110) cc_final: 0.7617 (mm110) REVERT: B 214 ARG cc_start: 0.8590 (mmm160) cc_final: 0.8318 (mmm-85) REVERT: B 261 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8584 (mp) REVERT: N 120 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8401 (mp10) REVERT: R 88 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.6129 (ttt180) REVERT: R 95 ASP cc_start: 0.8742 (m-30) cc_final: 0.8485 (m-30) REVERT: R 99 ILE cc_start: 0.8413 (pt) cc_final: 0.8182 (pp) outliers start: 25 outliers final: 16 residues processed: 148 average time/residue: 0.6151 time to fit residues: 96.3177 Evaluate side-chains 149 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 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 170 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 72 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 82 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.155580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.113661 restraints weight = 10211.117| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.49 r_work: 0.3338 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8187 Z= 0.186 Angle : 0.600 15.331 11087 Z= 0.307 Chirality : 0.044 0.244 1256 Planarity : 0.004 0.044 1411 Dihedral : 5.703 72.790 1114 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.35 % Allowed : 20.12 % Favored : 76.53 % 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 aren not related in a simple way. whole: 1.44 (0.27), residues: 997 helix: 2.63 (0.26), residues: 390 sheet: -0.24 (0.32), residues: 232 loop : 0.02 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.023 0.002 TYR N 60 PHE 0.014 0.002 PHE A 212 TRP 0.012 0.002 TRP A 234 HIS 0.008 0.001 HIS R 245 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 8186) covalent geometry : angle 0.59956 (11085) SS BOND : bond 0.00053 ( 1) SS BOND : angle 1.62777 ( 2) hydrogen bonds : bond 0.04200 ( 440) hydrogen bonds : angle 4.43473 ( 1257) *********************** 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 : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6906 (mptp) cc_final: 0.6650 (mptt) REVERT: A 370 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: B 16 ASN cc_start: 0.8177 (m-40) cc_final: 0.7746 (m-40) REVERT: B 46 ARG cc_start: 0.8011 (mtt180) cc_final: 0.7477 (mtm-85) REVERT: B 153 ASP cc_start: 0.8173 (m-30) cc_final: 0.7858 (p0) REVERT: B 214 ARG cc_start: 0.8586 (mmm160) cc_final: 0.8307 (mmm-85) REVERT: B 261 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8617 (mp) REVERT: N 120 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8433 (mp10) REVERT: R 88 ARG cc_start: 0.6640 (OUTLIER) cc_final: 0.6235 (ttt180) REVERT: R 95 ASP cc_start: 0.8768 (m-30) cc_final: 0.8532 (m-30) REVERT: R 99 ILE cc_start: 0.8501 (pt) cc_final: 0.8268 (pp) REVERT: R 326 PHE cc_start: 0.8449 (m-10) cc_final: 0.8161 (m-10) outliers start: 29 outliers final: 20 residues processed: 145 average time/residue: 0.5650 time to fit residues: 86.8328 Evaluate side-chains 147 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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 170 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.158271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.116765 restraints weight = 10120.172| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.48 r_work: 0.3381 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8187 Z= 0.115 Angle : 0.538 10.315 11087 Z= 0.281 Chirality : 0.042 0.248 1256 Planarity : 0.004 0.045 1411 Dihedral : 5.552 74.614 1114 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.89 % Allowed : 20.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.27), residues: 997 helix: 2.72 (0.25), residues: 388 sheet: -0.25 (0.32), residues: 232 loop : 0.01 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.027 0.001 TYR N 60 PHE 0.014 0.001 PHE A 212 TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS R 245 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8186) covalent geometry : angle 0.53739 (11085) SS BOND : bond 0.00035 ( 1) SS BOND : angle 1.49171 ( 2) hydrogen bonds : bond 0.03783 ( 440) hydrogen bonds : angle 4.23222 ( 1257) *********************** 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 157 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6913 (mptp) cc_final: 0.6698 (mptt) REVERT: A 32 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8593 (tttm) REVERT: A 370 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7936 (pm20) REVERT: A 386 MET cc_start: 0.8075 (mtm) cc_final: 0.7728 (ttm) REVERT: A 391 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.7875 (t80) REVERT: B 16 ASN cc_start: 0.8147 (m-40) cc_final: 0.7729 (m-40) REVERT: B 42 ARG cc_start: 0.7384 (ttt-90) cc_final: 0.6932 (ttp80) REVERT: B 46 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7423 (mtm-85) REVERT: B 153 ASP cc_start: 0.8158 (m-30) cc_final: 0.7862 (p0) REVERT: B 175 GLN cc_start: 0.7877 (mm110) cc_final: 0.7661 (mm110) REVERT: B 214 ARG cc_start: 0.8575 (mmm160) cc_final: 0.8294 (mmm-85) REVERT: B 261 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8571 (mp) REVERT: N 120 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8402 (mp10) REVERT: R 88 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.6118 (ttt180) REVERT: R 95 ASP cc_start: 0.8752 (m-30) cc_final: 0.8540 (m-30) REVERT: R 99 ILE cc_start: 0.8487 (pt) cc_final: 0.8261 (pp) REVERT: R 326 PHE cc_start: 0.8441 (m-10) cc_final: 0.8240 (m-10) outliers start: 25 outliers final: 16 residues processed: 146 average time/residue: 0.5956 time to fit residues: 92.2068 Evaluate side-chains 152 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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 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 12 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 59 optimal weight: 0.4980 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 64 optimal weight: 0.0970 chunk 75 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.159982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.118576 restraints weight = 10112.752| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.48 r_work: 0.3411 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8187 Z= 0.110 Angle : 0.545 11.201 11087 Z= 0.280 Chirality : 0.043 0.271 1256 Planarity : 0.003 0.045 1411 Dihedral : 5.424 75.018 1114 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.77 % Allowed : 21.39 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.27), residues: 997 helix: 2.73 (0.26), residues: 388 sheet: -0.23 (0.32), residues: 235 loop : 0.05 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.016 0.001 TYR R 156 PHE 0.013 0.001 PHE A 212 TRP 0.012 0.001 TRP A 234 HIS 0.008 0.001 HIS R 245 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8186) covalent geometry : angle 0.54511 (11085) SS BOND : bond 0.00032 ( 1) SS BOND : angle 1.48142 ( 2) hydrogen bonds : bond 0.03661 ( 440) hydrogen bonds : angle 4.15951 ( 1257) ********************** 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 156 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6838 (mptp) cc_final: 0.6628 (mptt) REVERT: A 32 LYS cc_start: 0.8867 (ttmm) cc_final: 0.8583 (tttm) REVERT: A 370 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7892 (pm20) REVERT: A 386 MET cc_start: 0.8037 (mtm) cc_final: 0.7677 (ttm) REVERT: A 391 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7841 (t80) REVERT: B 16 ASN cc_start: 0.8104 (m-40) cc_final: 0.7710 (m-40) REVERT: B 44 GLN cc_start: 0.8095 (tt0) cc_final: 0.7560 (pt0) REVERT: B 46 ARG cc_start: 0.7956 (mtt180) cc_final: 0.7392 (mtm-85) REVERT: B 153 ASP cc_start: 0.8161 (m-30) cc_final: 0.7858 (p0) REVERT: B 175 GLN cc_start: 0.7842 (mm110) cc_final: 0.7621 (mm110) REVERT: B 214 ARG cc_start: 0.8588 (mmm160) cc_final: 0.8301 (mmm-85) REVERT: B 261 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8516 (mp) REVERT: G 21 MET cc_start: 0.7181 (ttt) cc_final: 0.6969 (tmm) REVERT: N 120 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8354 (mp10) REVERT: R 88 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.6136 (ttt180) REVERT: R 95 ASP cc_start: 0.8727 (m-30) cc_final: 0.8518 (m-30) REVERT: R 99 ILE cc_start: 0.8408 (pt) cc_final: 0.8182 (pp) outliers start: 24 outliers final: 17 residues processed: 144 average time/residue: 0.5713 time to fit residues: 86.9281 Evaluate side-chains 150 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 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 170 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 0.0060 chunk 33 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.6002 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.157039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115293 restraints weight = 10162.641| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.48 r_work: 0.3368 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8187 Z= 0.158 Angle : 0.564 11.155 11087 Z= 0.294 Chirality : 0.044 0.265 1256 Planarity : 0.004 0.045 1411 Dihedral : 5.557 73.135 1114 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.66 % Allowed : 21.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.27), residues: 997 helix: 2.71 (0.25), residues: 388 sheet: -0.30 (0.32), residues: 235 loop : 0.00 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.025 0.002 TYR N 60 PHE 0.014 0.001 PHE A 212 TRP 0.012 0.001 TRP A 234 HIS 0.008 0.001 HIS R 245 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8186) covalent geometry : angle 0.56375 (11085) SS BOND : bond 0.00067 ( 1) SS BOND : angle 1.50566 ( 2) hydrogen bonds : bond 0.03998 ( 440) hydrogen bonds : angle 4.28711 ( 1257) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3849.79 seconds wall clock time: 65 minutes 50.61 seconds (3950.61 seconds total)