Starting phenix.real_space_refine on Fri Aug 22 17:10:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zoo_60314/08_2025/8zoo_60314.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zoo_60314/08_2025/8zoo_60314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zoo_60314/08_2025/8zoo_60314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zoo_60314/08_2025/8zoo_60314.map" model { file = "/net/cci-nas-00/data/ceres_data/8zoo_60314/08_2025/8zoo_60314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zoo_60314/08_2025/8zoo_60314.cif" } resolution = 3.14 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= 0.000 sd= 0.008 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 P 3 5.49 5 S 30 5.16 5 C 3883 2.51 5 N 1124 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6272 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3099 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Chain: "B" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3116 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 12, 'TRANS': 403} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'NAP': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'VHF:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.55, per 1000 atoms: 0.25 Number of scatterers: 6272 At special positions: 0 Unit cell: (99.64, 110.24, 61.48, 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) S 30 16.00 P 3 15.00 O 1232 8.00 N 1124 7.00 C 3883 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 330.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1540 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 53.2% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 38 through 57 removed outlier: 3.526A pdb=" N ILE A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 67 Processing helix chain 'A' and resid 69 through 85 removed outlier: 3.545A pdb=" N ASN A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 137 removed outlier: 4.018A pdb=" N THR A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 166 Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 180 through 189 Processing helix chain 'A' and resid 206 through 213 Processing helix chain 'A' and resid 234 through 248 removed outlier: 3.740A pdb=" N GLN A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 281 removed outlier: 4.385A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.767A pdb=" N GLU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 348 through 359 Processing helix chain 'A' and resid 370 through 373 removed outlier: 3.799A pdb=" N THR A 373 " --> pdb=" O THR A 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 373' Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'B' and resid 3 through 18 removed outlier: 3.636A pdb=" N LYS B 15 " --> pdb=" O GLN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 38 removed outlier: 3.557A pdb=" N LYS B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 56 removed outlier: 3.613A pdb=" N ILE B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 69 through 85 Processing helix chain 'B' and resid 123 through 137 removed outlier: 4.026A pdb=" N VAL B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 167 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 180 through 190 removed outlier: 3.747A pdb=" N VAL B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 212 Processing helix chain 'B' and resid 234 through 248 removed outlier: 3.734A pdb=" N GLN B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 281 removed outlier: 3.937A pdb=" N ASP B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Proline residue: B 271 - end of helix removed outlier: 3.528A pdb=" N GLU B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.099A pdb=" N ALA B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLN B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 325 through 337 Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 370 through 373 removed outlier: 3.785A pdb=" N THR B 373 " --> pdb=" O THR B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 373' Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 98 removed outlier: 6.895A pdb=" N VAL A 93 " --> pdb=" O ARG A 109 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG A 109 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP A 95 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ALA B 368 " --> pdb=" O GLY A 411 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR A 413 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP B 342 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ASN B 367 " --> pdb=" O ASP B 342 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE B 344 " --> pdb=" O ASN B 367 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS B 226 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU B 345 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR B 228 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N CYS B 225 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 258 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU B 257 " --> pdb=" O ASP B 317 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU B 284 " --> pdb=" O VAL B 302 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 175 removed outlier: 3.512A pdb=" N MET A 196 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 303 removed outlier: 6.243A pdb=" N LEU A 284 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU A 257 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N CYS A 225 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU A 260 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 227 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASN A 262 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL A 229 " --> pdb=" O ASN A 262 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS A 226 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU A 345 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR A 228 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP A 342 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ASN A 367 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE A 344 " --> pdb=" O ASN A 367 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 364 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLY B 411 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 366 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N TYR B 413 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA A 368 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP B 95 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG B 109 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL B 93 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 387 Processing sheet with id=AA5, first strand: chain 'B' and resid 173 through 176 Processing sheet with id=AA6, first strand: chain 'B' and resid 386 through 387 346 hydrogen bonds defined for protein. 999 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: 0.71 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1115 1.31 - 1.44: 1416 1.44 - 1.56: 3758 1.56 - 1.69: 5 1.69 - 1.82: 46 Bond restraints: 6340 Sorted by residual: bond pdb=" O2B NAP B 501 " pdb=" P2B NAP B 501 " ideal model delta sigma weight residual 1.736 1.617 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C5D NAP B 501 " pdb=" O5D NAP B 501 " ideal model delta sigma weight residual 1.403 1.449 -0.046 2.00e-02 2.50e+03 5.34e+00 bond pdb=" O5D NAP B 501 " pdb=" PN NAP B 501 " ideal model delta sigma weight residual 1.649 1.603 0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" N ASP B 100 " pdb=" CA ASP B 100 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.81e+00 bond pdb=" O3 NAP B 501 " pdb=" PA NAP B 501 " ideal model delta sigma weight residual 1.647 1.603 0.044 2.00e-02 2.50e+03 4.79e+00 ... (remaining 6335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 8435 1.81 - 3.62: 131 3.62 - 5.43: 28 5.43 - 7.25: 2 7.25 - 9.06: 2 Bond angle restraints: 8598 Sorted by residual: angle pdb=" CB MET A 62 " pdb=" CG MET A 62 " pdb=" SD MET A 62 " ideal model delta sigma weight residual 112.70 121.76 -9.06 3.00e+00 1.11e-01 9.12e+00 angle pdb=" CA ASP B 100 " pdb=" C ASP B 100 " pdb=" O ASP B 100 " ideal model delta sigma weight residual 120.82 118.09 2.73 1.05e+00 9.07e-01 6.77e+00 angle pdb=" N ASP B 100 " pdb=" CA ASP B 100 " pdb=" C ASP B 100 " ideal model delta sigma weight residual 111.07 108.30 2.77 1.07e+00 8.73e-01 6.68e+00 angle pdb=" CA ASP A 95 " pdb=" C ASP A 95 " pdb=" O ASP A 95 " ideal model delta sigma weight residual 121.31 118.57 2.74 1.07e+00 8.73e-01 6.57e+00 angle pdb=" C ASP A 78 " pdb=" N ASP A 79 " pdb=" CA ASP A 79 " ideal model delta sigma weight residual 121.14 116.99 4.15 1.75e+00 3.27e-01 5.62e+00 ... (remaining 8593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 3415 17.20 - 34.39: 382 34.39 - 51.59: 99 51.59 - 68.78: 45 68.78 - 85.98: 13 Dihedral angle restraints: 3954 sinusoidal: 1573 harmonic: 2381 Sorted by residual: dihedral pdb=" CA ASN B 152 " pdb=" CB ASN B 152 " pdb=" CG ASN B 152 " pdb=" OD1 ASN B 152 " ideal model delta sinusoidal sigma weight residual -90.00 -160.78 70.78 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CG ARG B 334 " pdb=" CD ARG B 334 " pdb=" NE ARG B 334 " pdb=" CZ ARG B 334 " ideal model delta sinusoidal sigma weight residual 90.00 134.97 -44.97 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG A 65 " pdb=" CD ARG A 65 " pdb=" NE ARG A 65 " pdb=" CZ ARG A 65 " ideal model delta sinusoidal sigma weight residual 180.00 136.45 43.55 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 3951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 788 0.044 - 0.088: 174 0.088 - 0.131: 68 0.131 - 0.175: 4 0.175 - 0.219: 2 Chirality restraints: 1036 Sorted by residual: chirality pdb=" CB ILE A 31 " pdb=" CA ILE A 31 " pdb=" CG1 ILE A 31 " pdb=" CG2 ILE A 31 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C3B NAP B 501 " pdb=" C2B NAP B 501 " pdb=" C4B NAP B 501 " pdb=" O3B NAP B 501 " both_signs ideal model delta sigma weight residual False -2.52 -2.73 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C4D NAP B 501 " pdb=" C3D NAP B 501 " pdb=" C5D NAP B 501 " pdb=" O4D NAP B 501 " both_signs ideal model delta sigma weight residual False -2.58 -2.43 -0.16 2.00e-01 2.50e+01 6.17e-01 ... (remaining 1033 not shown) Planarity restraints: 1121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 360 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" CG ASP A 360 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP A 360 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 360 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 360 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C ASP A 360 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP A 360 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 361 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 215 " -0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO B 216 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 216 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 216 " -0.016 5.00e-02 4.00e+02 ... (remaining 1118 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1367 2.79 - 3.31: 6154 3.31 - 3.84: 10305 3.84 - 4.37: 11667 4.37 - 4.90: 20744 Nonbonded interactions: 50237 Sorted by model distance: nonbonded pdb=" O PRO B 271 " pdb=" OG SER B 274 " model vdw 2.257 3.040 nonbonded pdb=" OD2 ASP A 342 " pdb=" OG SER A 361 " model vdw 2.277 3.040 nonbonded pdb=" OG SER B 20 " pdb=" OE1 GLU B 23 " model vdw 2.282 3.040 nonbonded pdb=" OE1 GLU B 312 " pdb=" O3D NAP B 501 " model vdw 2.305 3.040 nonbonded pdb=" OE1 GLN A 248 " pdb=" NH2 ARG A 371 " model vdw 2.321 3.120 ... (remaining 50232 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 2 through 200 or resid 205 through 417)) } 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.520 Find NCS groups from input model: 0.060 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 0.119 6341 Z= 0.207 Angle : 0.573 9.057 8598 Z= 0.297 Chirality : 0.043 0.219 1036 Planarity : 0.003 0.028 1121 Dihedral : 17.432 85.979 2414 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 20.09 % Favored : 79.91 % 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: 1.66 (0.30), residues: 822 helix: 2.63 (0.27), residues: 387 sheet: 0.68 (0.46), residues: 132 loop : -0.77 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.010 0.001 TYR B 119 PHE 0.003 0.001 PHE A 372 TRP 0.008 0.002 TRP A 407 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 6340) covalent geometry : angle 0.57265 ( 8598) hydrogen bonds : bond 0.15150 ( 346) hydrogen bonds : angle 5.72615 ( 999) Misc. bond : bond 0.04917 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.245 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0607 time to fit residues: 4.7041 Evaluate side-chains 51 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.088004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.062644 restraints weight = 15196.888| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 4.08 r_work: 0.2751 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6341 Z= 0.141 Angle : 0.465 8.141 8598 Z= 0.243 Chirality : 0.042 0.163 1036 Planarity : 0.003 0.028 1121 Dihedral : 7.525 56.752 966 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.96 % Allowed : 18.13 % Favored : 79.91 % 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: 1.89 (0.30), residues: 822 helix: 2.82 (0.27), residues: 393 sheet: 0.72 (0.46), residues: 131 loop : -0.71 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.006 0.001 TYR B 405 PHE 0.005 0.001 PHE B 355 TRP 0.008 0.002 TRP A 407 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6340) covalent geometry : angle 0.46463 ( 8598) hydrogen bonds : bond 0.03587 ( 346) hydrogen bonds : angle 4.43461 ( 999) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 196 MET cc_start: 0.8528 (tmm) cc_final: 0.7893 (tmm) REVERT: A 277 MET cc_start: 0.8958 (tpp) cc_final: 0.8576 (tpp) REVERT: A 360 ASP cc_start: 0.8762 (t0) cc_final: 0.8436 (t0) REVERT: B 415 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8589 (pt) outliers start: 13 outliers final: 6 residues processed: 64 average time/residue: 0.0531 time to fit residues: 5.0018 Evaluate side-chains 57 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 415 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 6 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.087211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.061638 restraints weight = 15223.290| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 4.06 r_work: 0.2712 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6341 Z= 0.202 Angle : 0.498 8.064 8598 Z= 0.261 Chirality : 0.042 0.152 1036 Planarity : 0.003 0.027 1121 Dihedral : 6.800 54.366 966 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.17 % Allowed : 17.98 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.30), residues: 822 helix: 2.87 (0.27), residues: 393 sheet: 0.70 (0.45), residues: 131 loop : -0.80 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.008 0.001 TYR B 119 PHE 0.006 0.001 PHE B 313 TRP 0.009 0.002 TRP A 407 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 6340) covalent geometry : angle 0.49761 ( 8598) hydrogen bonds : bond 0.03843 ( 346) hydrogen bonds : angle 4.35784 ( 999) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8783 (mtm) cc_final: 0.8474 (mtt) REVERT: A 196 MET cc_start: 0.8681 (tmm) cc_final: 0.7986 (tmm) REVERT: A 265 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8980 (tp) REVERT: A 277 MET cc_start: 0.9031 (tpp) cc_final: 0.8790 (tpp) REVERT: A 360 ASP cc_start: 0.8824 (t0) cc_final: 0.8445 (t0) REVERT: B 234 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: B 415 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8644 (pt) outliers start: 21 outliers final: 10 residues processed: 68 average time/residue: 0.0580 time to fit residues: 5.6032 Evaluate side-chains 60 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 415 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 63 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.084641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.059029 restraints weight = 15529.174| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 4.10 r_work: 0.2674 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 6341 Z= 0.291 Angle : 0.558 7.358 8598 Z= 0.293 Chirality : 0.044 0.145 1036 Planarity : 0.004 0.027 1121 Dihedral : 6.622 53.191 966 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.78 % Allowed : 18.28 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.30), residues: 822 helix: 2.71 (0.26), residues: 392 sheet: 0.62 (0.47), residues: 127 loop : -0.99 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.013 0.001 TYR B 119 PHE 0.009 0.001 PHE B 313 TRP 0.011 0.003 TRP A 407 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00670 ( 6340) covalent geometry : angle 0.55832 ( 8598) hydrogen bonds : bond 0.04233 ( 346) hydrogen bonds : angle 4.50665 ( 999) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8962 (mtm) cc_final: 0.8520 (mtp) REVERT: A 193 TYR cc_start: 0.8812 (m-10) cc_final: 0.8608 (m-10) REVERT: A 196 MET cc_start: 0.8766 (tmm) cc_final: 0.7984 (tmm) REVERT: A 265 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8991 (tp) REVERT: A 360 ASP cc_start: 0.8857 (t0) cc_final: 0.8473 (t0) REVERT: B 104 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8015 (mmt180) REVERT: B 234 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6975 (mp0) outliers start: 25 outliers final: 15 residues processed: 68 average time/residue: 0.0592 time to fit residues: 5.7344 Evaluate side-chains 64 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 234 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 1 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.087522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.061942 restraints weight = 15527.907| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 4.11 r_work: 0.2723 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6341 Z= 0.132 Angle : 0.471 9.219 8598 Z= 0.242 Chirality : 0.041 0.155 1036 Planarity : 0.003 0.030 1121 Dihedral : 6.048 43.070 966 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.66 % Allowed : 20.09 % Favored : 78.25 % 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: 1.87 (0.30), residues: 822 helix: 2.90 (0.26), residues: 392 sheet: 0.69 (0.45), residues: 131 loop : -0.84 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.006 0.001 TYR A 119 PHE 0.003 0.001 PHE B 355 TRP 0.008 0.002 TRP A 407 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6340) covalent geometry : angle 0.47072 ( 8598) hydrogen bonds : bond 0.03277 ( 346) hydrogen bonds : angle 4.18570 ( 999) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8802 (mtm) cc_final: 0.8392 (mtp) REVERT: A 196 MET cc_start: 0.8688 (tmm) cc_final: 0.7968 (tmm) REVERT: A 265 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8969 (tp) REVERT: A 277 MET cc_start: 0.8995 (tpp) cc_final: 0.8599 (tpp) REVERT: A 360 ASP cc_start: 0.8881 (t0) cc_final: 0.8499 (t0) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.0550 time to fit residues: 4.9964 Evaluate side-chains 62 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 186 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.062915 restraints weight = 15356.727| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 4.14 r_work: 0.2758 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6341 Z= 0.093 Angle : 0.450 8.857 8598 Z= 0.230 Chirality : 0.041 0.151 1036 Planarity : 0.003 0.031 1121 Dihedral : 5.344 34.552 966 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.81 % Allowed : 20.69 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.30), residues: 822 helix: 2.97 (0.27), residues: 392 sheet: 0.75 (0.45), residues: 132 loop : -0.69 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 54 TYR 0.008 0.001 TYR B 405 PHE 0.004 0.001 PHE B 355 TRP 0.006 0.001 TRP A 407 HIS 0.003 0.000 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 6340) covalent geometry : angle 0.45039 ( 8598) hydrogen bonds : bond 0.02767 ( 346) hydrogen bonds : angle 3.97693 ( 999) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.150 Fit side-chains REVERT: A 136 THR cc_start: 0.9236 (t) cc_final: 0.9002 (t) REVERT: A 190 MET cc_start: 0.8697 (mtm) cc_final: 0.8403 (mtp) REVERT: A 196 MET cc_start: 0.8587 (tmm) cc_final: 0.7988 (tmm) REVERT: A 265 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8974 (tp) REVERT: A 277 MET cc_start: 0.9138 (tpp) cc_final: 0.8901 (tpp) REVERT: A 360 ASP cc_start: 0.8768 (t0) cc_final: 0.8442 (t0) outliers start: 12 outliers final: 7 residues processed: 62 average time/residue: 0.0433 time to fit residues: 4.1176 Evaluate side-chains 57 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 215 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.086407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.060882 restraints weight = 15419.376| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 4.12 r_work: 0.2716 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6341 Z= 0.184 Angle : 0.498 8.165 8598 Z= 0.254 Chirality : 0.042 0.144 1036 Planarity : 0.003 0.031 1121 Dihedral : 5.439 34.179 966 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.11 % Allowed : 21.75 % Favored : 76.13 % 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: 1.97 (0.30), residues: 822 helix: 2.93 (0.27), residues: 392 sheet: 0.77 (0.45), residues: 132 loop : -0.74 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 81 TYR 0.006 0.001 TYR A 119 PHE 0.005 0.001 PHE B 313 TRP 0.008 0.002 TRP A 407 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 6340) covalent geometry : angle 0.49809 ( 8598) hydrogen bonds : bond 0.03388 ( 346) hydrogen bonds : angle 4.08724 ( 999) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.303 Fit side-chains REVERT: A 190 MET cc_start: 0.8806 (mtm) cc_final: 0.8508 (mtp) REVERT: A 196 MET cc_start: 0.8712 (tmm) cc_final: 0.7965 (tmm) REVERT: A 265 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8972 (tp) REVERT: A 360 ASP cc_start: 0.8868 (t0) cc_final: 0.8498 (t0) outliers start: 14 outliers final: 10 residues processed: 60 average time/residue: 0.0604 time to fit residues: 5.4063 Evaluate side-chains 58 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 243 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 7 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 80 optimal weight: 0.0870 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.088674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.063535 restraints weight = 15345.120| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 4.06 r_work: 0.2765 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6341 Z= 0.105 Angle : 0.467 8.857 8598 Z= 0.236 Chirality : 0.041 0.150 1036 Planarity : 0.003 0.032 1121 Dihedral : 5.167 35.308 966 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.11 % Allowed : 21.45 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.30), residues: 822 helix: 2.93 (0.27), residues: 393 sheet: 0.73 (0.45), residues: 138 loop : -0.69 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 150 TYR 0.007 0.001 TYR B 405 PHE 0.004 0.001 PHE B 355 TRP 0.007 0.002 TRP A 407 HIS 0.002 0.000 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6340) covalent geometry : angle 0.46741 ( 8598) hydrogen bonds : bond 0.02842 ( 346) hydrogen bonds : angle 3.94965 ( 999) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.214 Fit side-chains REVERT: A 136 THR cc_start: 0.9231 (t) cc_final: 0.8980 (t) REVERT: A 190 MET cc_start: 0.8694 (mtm) cc_final: 0.8371 (mtp) REVERT: A 196 MET cc_start: 0.8608 (tmm) cc_final: 0.7905 (tmm) REVERT: A 265 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8985 (tp) REVERT: A 360 ASP cc_start: 0.8803 (t0) cc_final: 0.8466 (t0) outliers start: 14 outliers final: 9 residues processed: 61 average time/residue: 0.0503 time to fit residues: 4.6036 Evaluate side-chains 58 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 215 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 76 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.085600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.060352 restraints weight = 15536.633| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 4.10 r_work: 0.2710 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6341 Z= 0.218 Angle : 0.536 9.009 8598 Z= 0.276 Chirality : 0.042 0.139 1036 Planarity : 0.003 0.030 1121 Dihedral : 5.460 34.540 966 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.96 % Allowed : 22.05 % Favored : 75.98 % 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: 1.92 (0.30), residues: 822 helix: 2.87 (0.27), residues: 392 sheet: 0.73 (0.44), residues: 138 loop : -0.76 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 334 TYR 0.011 0.001 TYR B 119 PHE 0.005 0.001 PHE B 313 TRP 0.007 0.002 TRP A 407 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 6340) covalent geometry : angle 0.53649 ( 8598) hydrogen bonds : bond 0.03595 ( 346) hydrogen bonds : angle 4.15516 ( 999) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.164 Fit side-chains REVERT: A 190 MET cc_start: 0.8863 (mtm) cc_final: 0.8542 (mtp) REVERT: A 196 MET cc_start: 0.8743 (tmm) cc_final: 0.7983 (tmm) REVERT: A 265 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8991 (tp) REVERT: A 277 MET cc_start: 0.8966 (tpp) cc_final: 0.8706 (tpp) REVERT: A 360 ASP cc_start: 0.8928 (t0) cc_final: 0.8561 (t0) REVERT: B 234 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6920 (mp0) outliers start: 13 outliers final: 10 residues processed: 60 average time/residue: 0.0515 time to fit residues: 4.5518 Evaluate side-chains 60 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 243 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 28 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 59 optimal weight: 0.0570 chunk 29 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 66 optimal weight: 0.0000 chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.6108 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.087087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.061715 restraints weight = 15329.652| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.10 r_work: 0.2736 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6341 Z= 0.139 Angle : 0.501 8.817 8598 Z= 0.255 Chirality : 0.042 0.148 1036 Planarity : 0.003 0.031 1121 Dihedral : 5.297 35.306 966 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.81 % Allowed : 22.51 % Favored : 75.68 % 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: 1.95 (0.30), residues: 822 helix: 2.88 (0.27), residues: 392 sheet: 0.86 (0.44), residues: 135 loop : -0.75 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.006 0.001 TYR B 119 PHE 0.003 0.001 PHE B 313 TRP 0.007 0.002 TRP A 407 HIS 0.003 0.000 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6340) covalent geometry : angle 0.50088 ( 8598) hydrogen bonds : bond 0.03163 ( 346) hydrogen bonds : angle 4.04255 ( 999) Misc. bond : bond 0.00004 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.227 Fit side-chains REVERT: A 190 MET cc_start: 0.8742 (mtm) cc_final: 0.8419 (mtp) REVERT: A 196 MET cc_start: 0.8696 (tmm) cc_final: 0.7946 (tmm) REVERT: A 265 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8980 (tp) REVERT: A 277 MET cc_start: 0.8953 (tpp) cc_final: 0.8678 (tpp) REVERT: A 360 ASP cc_start: 0.8893 (t0) cc_final: 0.8533 (t0) outliers start: 12 outliers final: 11 residues processed: 57 average time/residue: 0.0452 time to fit residues: 3.9631 Evaluate side-chains 58 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 243 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.088720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.063624 restraints weight = 15247.662| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.06 r_work: 0.2769 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6341 Z= 0.107 Angle : 0.485 8.984 8598 Z= 0.245 Chirality : 0.041 0.148 1036 Planarity : 0.003 0.032 1121 Dihedral : 5.074 36.353 966 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.51 % Allowed : 23.11 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.31), residues: 822 helix: 2.97 (0.27), residues: 391 sheet: 0.55 (0.44), residues: 142 loop : -0.67 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 150 TYR 0.010 0.001 TYR B 119 PHE 0.004 0.001 PHE B 355 TRP 0.006 0.001 TRP A 407 HIS 0.003 0.000 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 6340) covalent geometry : angle 0.48530 ( 8598) hydrogen bonds : bond 0.02839 ( 346) hydrogen bonds : angle 3.93670 ( 999) Misc. bond : bond 0.00000 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1312.88 seconds wall clock time: 23 minutes 9.31 seconds (1389.31 seconds total)