Starting phenix.real_space_refine on Thu Jul 2 10:21:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z2h_14466/07_2026/7z2h_14466.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2h_14466/07_2026/7z2h_14466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z2h_14466/07_2026/7z2h_14466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2h_14466/07_2026/7z2h_14466.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z2h_14466/07_2026/7z2h_14466.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z2h_14466/07_2026/7z2h_14466.cif" model { file = "/net/cci-nas-00/data/ceres_data/7z2h_14466/07_2026/7z2h_14466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2h_14466/07_2026/7z2h_14466.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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: 7 Type Number sf(0) Gaussians P 36 5.49 5 S 13 5.16 5 Cl 1 4.86 5 C 5333 2.51 5 N 1405 2.21 5 O 1623 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8414 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4254 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 489} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3390 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 741 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'2KW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.41, per 1000 atoms: 0.17 Number of scatterers: 8414 At special positions: 0 Unit cell: (97, 110.58, 96.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 13 16.00 P 36 15.00 F 3 9.00 O 1623 8.00 N 1405 7.00 C 5333 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=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 353.2 milliseconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 39.7% alpha, 10.9% beta 13 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 35 through 44 removed outlier: 3.558A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 42 " --> pdb=" O CYS A 38 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.790A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.934A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.329A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 384 removed outlier: 3.720A pdb=" N GLN A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 405 Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 499 through 508 removed outlier: 4.184A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 544 through 552 removed outlier: 3.592A pdb=" N VAL A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.747A pdb=" N GLU B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 removed outlier: 6.508A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.722A pdb=" N LYS B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.929A pdb=" N VAL B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.746A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.622A pdb=" N LYS B 138 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 175 removed outlier: 4.288A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.520A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.729A pdb=" N TRP B 239 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 269 removed outlier: 3.783A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 364 through 383 removed outlier: 3.561A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.770A pdb=" N TRP B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 406 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 4.014A pdb=" N ARG A 143 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 107 Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 234 Processing sheet with id=AA4, first strand: chain 'A' and resid 252 through 253 removed outlier: 4.426A pdb=" N TRP A 252 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331 removed outlier: 6.718A pdb=" N TRP A 337 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS A 353 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA7, first strand: chain 'A' and resid 438 through 441 removed outlier: 4.193A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 532 " --> pdb=" O VAL A 493 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 444 through 445 Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 49 removed outlier: 3.768A pdb=" N ILE B 142 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 132 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 105 through 110 Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.691A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 348 through 355 removed outlier: 3.797A pdb=" N TYR B 339 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B 325 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LYS B 390 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA B 327 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1304 1.27 - 1.40: 2156 1.40 - 1.54: 5045 1.54 - 1.67: 181 1.67 - 1.81: 24 Bond restraints: 8710 Sorted by residual: bond pdb=" C10 2KW A 601 " pdb=" C9 2KW A 601 " ideal model delta sigma weight residual 1.354 1.522 -0.168 2.00e-02 2.50e+03 7.08e+01 bond pdb=" C21 2KW A 601 " pdb=" N20 2KW A 601 " ideal model delta sigma weight residual 1.356 1.500 -0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C10 2KW A 601 " pdb=" N11 2KW A 601 " ideal model delta sigma weight residual 1.355 1.489 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C7 2KW A 601 " pdb=" C8 2KW A 601 " ideal model delta sigma weight residual 1.359 1.485 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C4' DC E 3 " pdb=" O4' DC E 3 " ideal model delta sigma weight residual 1.446 1.506 -0.060 1.00e-02 1.00e+04 3.66e+01 ... (remaining 8705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 11850 3.04 - 6.08: 128 6.08 - 9.13: 14 9.13 - 12.17: 2 12.17 - 15.21: 3 Bond angle restraints: 11997 Sorted by residual: angle pdb=" C LEU A 228 " pdb=" CA LEU A 228 " pdb=" CB LEU A 228 " ideal model delta sigma weight residual 110.24 122.50 -12.26 1.46e+00 4.69e-01 7.05e+01 angle pdb=" N LEU A 228 " pdb=" CA LEU A 228 " pdb=" C LEU A 228 " ideal model delta sigma weight residual 108.13 94.42 13.71 1.72e+00 3.38e-01 6.35e+01 angle pdb=" C ASP A 186 " pdb=" CA ASP A 186 " pdb=" CB ASP A 186 " ideal model delta sigma weight residual 109.33 94.12 15.21 1.97e+00 2.58e-01 5.96e+01 angle pdb=" O4' DC E 3 " pdb=" C4' DC E 3 " pdb=" C3' DC E 3 " ideal model delta sigma weight residual 106.00 101.95 4.05 6.00e-01 2.78e+00 4.56e+01 angle pdb=" N TRP B 426 " pdb=" CA TRP B 426 " pdb=" C TRP B 426 " ideal model delta sigma weight residual 112.89 105.54 7.35 1.24e+00 6.50e-01 3.51e+01 ... (remaining 11992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4325 17.77 - 35.55: 532 35.55 - 53.32: 171 53.32 - 71.10: 49 71.10 - 88.87: 11 Dihedral angle restraints: 5088 sinusoidal: 2354 harmonic: 2734 Sorted by residual: dihedral pdb=" C ASP A 186 " pdb=" N ASP A 186 " pdb=" CA ASP A 186 " pdb=" CB ASP A 186 " ideal model delta harmonic sigma weight residual -122.60 -105.98 -16.62 0 2.50e+00 1.60e-01 4.42e+01 dihedral pdb=" C MET A 164 " pdb=" N MET A 164 " pdb=" CA MET A 164 " pdb=" CB MET A 164 " ideal model delta harmonic sigma weight residual -122.60 -135.65 13.05 0 2.50e+00 1.60e-01 2.73e+01 dihedral pdb=" N MET A 164 " pdb=" C MET A 164 " pdb=" CA MET A 164 " pdb=" CB MET A 164 " ideal model delta harmonic sigma weight residual 122.80 134.93 -12.13 0 2.50e+00 1.60e-01 2.35e+01 ... (remaining 5085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1280 0.125 - 0.250: 25 0.250 - 0.376: 3 0.376 - 0.501: 0 0.501 - 0.626: 2 Chirality restraints: 1310 Sorted by residual: chirality pdb=" P DA E -2 " pdb=" OP1 DA E -2 " pdb=" OP2 DA E -2 " pdb=" O5' DA E -2 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.63 2.00e-01 2.50e+01 9.79e+00 chirality pdb=" CA MET A 164 " pdb=" N MET A 164 " pdb=" C MET A 164 " pdb=" CB MET A 164 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.17 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1307 not shown) Planarity restraints: 1382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 125 " -0.565 9.50e-02 1.11e+02 2.53e-01 3.93e+01 pdb=" NE ARG A 125 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 125 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 125 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 125 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 118 " 0.063 5.00e-02 4.00e+02 9.35e-02 1.40e+01 pdb=" N PRO B 119 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 187 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C LEU A 187 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU A 187 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR A 188 " 0.017 2.00e-02 2.50e+03 ... (remaining 1379 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2009 2.80 - 3.32: 7739 3.32 - 3.85: 14183 3.85 - 4.37: 16225 4.37 - 4.90: 26618 Nonbonded interactions: 66774 Sorted by model distance: nonbonded pdb=" O GLY B 196 " pdb=" OG1 THR B 200 " model vdw 2.274 3.040 nonbonded pdb=" O 2KW A 601 " pdb=" F15 2KW A 601 " model vdw 2.293 2.990 nonbonded pdb=" O ARG A 277 " pdb=" N SER A 280 " model vdw 2.326 3.120 nonbonded pdb=" OG1 THR A 376 " pdb=" OG1 THR A 386 " model vdw 2.344 3.040 nonbonded pdb=" NZ LYS A 13 " pdb=" O LYS A 82 " model vdw 2.377 3.120 ... (remaining 66769 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 group one per residue 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: 0.140 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.630 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 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 : 0.006 0.168 8710 Z= 0.334 Angle : 0.798 15.210 11997 Z= 0.474 Chirality : 0.056 0.626 1310 Planarity : 0.009 0.253 1382 Dihedral : 17.826 88.870 3322 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.34 % Favored : 95.55 % Rotamer: Outliers : 0.72 % Allowed : 0.84 % Favored : 98.44 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.28), residues: 921 helix: 0.86 (0.31), residues: 308 sheet: -1.63 (0.42), residues: 149 loop : -0.94 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 277 TYR 0.027 0.001 TYR A 232 PHE 0.012 0.001 PHE A 124 TRP 0.023 0.002 TRP B 414 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.33 ( 8710) covalent geometry : angle 0.79767 / 0.47 (11997) hydrogen bonds : bond 0.14525 / 9.74 ( 313) hydrogen bonds : angle 7.87090 / 5.62 ( 828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.7794 (m-10) cc_final: 0.7447 (m-10) REVERT: B 180 ILE cc_start: 0.7335 (mm) cc_final: 0.6877 (tt) REVERT: B 198 HIS cc_start: 0.4680 (t70) cc_final: 0.4389 (t70) REVERT: B 409 THR cc_start: 0.7210 (m) cc_final: 0.6812 (p) outliers start: 6 outliers final: 2 residues processed: 133 average time/residue: 0.0742 time to fit residues: 14.0046 Evaluate side-chains 108 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain B residue 32 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 255 ASN B 269 GLN B 418 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.223499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.178615 restraints weight = 9988.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.183107 restraints weight = 6280.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.186104 restraints weight = 4692.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.187552 restraints weight = 3918.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.188954 restraints weight = 3547.700| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8710 Z= 0.176 Angle : 0.665 9.087 11997 Z= 0.356 Chirality : 0.046 0.172 1310 Planarity : 0.005 0.055 1382 Dihedral : 17.033 77.083 1371 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.13 % Favored : 95.77 % Rotamer: Outliers : 0.36 % Allowed : 8.38 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.28), residues: 921 helix: 0.99 (0.30), residues: 309 sheet: -1.64 (0.42), residues: 145 loop : -0.95 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 125 TYR 0.018 0.002 TYR A 501 PHE 0.015 0.002 PHE A 124 TRP 0.019 0.002 TRP B 402 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 ( 8710) covalent geometry : angle 0.66520 / 0.36 (11997) hydrogen bonds : bond 0.04507 / 2.96 ( 313) hydrogen bonds : angle 5.25993 / 3.50 ( 828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: B 180 ILE cc_start: 0.7429 (mm) cc_final: 0.6988 (tt) REVERT: B 409 THR cc_start: 0.7273 (m) cc_final: 0.6853 (p) outliers start: 3 outliers final: 3 residues processed: 115 average time/residue: 0.0650 time to fit residues: 11.1960 Evaluate side-chains 105 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 13 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 39 optimal weight: 0.0030 chunk 54 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 0.0270 chunk 34 optimal weight: 9.9990 overall best weight: 3.6054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.221170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.173746 restraints weight = 9910.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.178628 restraints weight = 6055.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.181781 restraints weight = 4444.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.183792 restraints weight = 3674.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.184733 restraints weight = 3273.063| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8710 Z= 0.150 Angle : 0.615 8.850 11997 Z= 0.330 Chirality : 0.044 0.178 1310 Planarity : 0.005 0.050 1382 Dihedral : 16.839 76.070 1371 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.13 % Favored : 95.77 % Rotamer: Outliers : 1.68 % Allowed : 10.30 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.28), residues: 921 helix: 1.17 (0.30), residues: 306 sheet: -1.65 (0.42), residues: 145 loop : -0.97 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.014 0.002 TYR A 457 PHE 0.012 0.002 PHE A 124 TRP 0.021 0.002 TRP B 402 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 8710) covalent geometry : angle 0.61545 / 0.33 (11997) hydrogen bonds : bond 0.04036 / 2.63 ( 313) hydrogen bonds : angle 5.08389 / 3.35 ( 828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 278 GLN cc_start: 0.6803 (tp40) cc_final: 0.6524 (mm-40) REVERT: B 180 ILE cc_start: 0.7486 (mm) cc_final: 0.7032 (tt) REVERT: B 409 THR cc_start: 0.7140 (m) cc_final: 0.6765 (p) outliers start: 14 outliers final: 8 residues processed: 126 average time/residue: 0.0642 time to fit residues: 12.0050 Evaluate side-chains 110 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 396 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 0.0770 chunk 69 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 30 optimal weight: 0.0070 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 50.0000 chunk 90 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 0.0010 chunk 76 optimal weight: 5.9990 overall best weight: 0.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 GLN B 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.225819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.181155 restraints weight = 9918.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.185727 restraints weight = 6179.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.188783 restraints weight = 4564.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.190744 restraints weight = 3790.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.191615 restraints weight = 3381.008| |-----------------------------------------------------------------------------| r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8710 Z= 0.120 Angle : 0.565 8.285 11997 Z= 0.305 Chirality : 0.042 0.179 1310 Planarity : 0.004 0.046 1382 Dihedral : 16.563 75.651 1369 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 1.68 % Allowed : 11.62 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.28), residues: 921 helix: 1.21 (0.30), residues: 320 sheet: -1.39 (0.41), residues: 155 loop : -0.96 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 143 TYR 0.012 0.001 TYR B 354 PHE 0.007 0.001 PHE A 124 TRP 0.013 0.001 TRP B 402 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 ( 8710) covalent geometry : angle 0.56515 / 0.30 (11997) hydrogen bonds : bond 0.03247 / 2.10 ( 313) hydrogen bonds : angle 4.78449 / 3.14 ( 828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 LEU cc_start: 0.8356 (mm) cc_final: 0.8140 (mm) REVERT: A 281 LYS cc_start: 0.5286 (mmtt) cc_final: 0.5046 (mmtt) REVERT: B 180 ILE cc_start: 0.7448 (mm) cc_final: 0.6991 (tt) outliers start: 14 outliers final: 9 residues processed: 125 average time/residue: 0.0857 time to fit residues: 15.5986 Evaluate side-chains 109 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 10 optimal weight: 0.3980 chunk 78 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 79 optimal weight: 30.0000 chunk 91 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.221380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.175682 restraints weight = 9908.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.179149 restraints weight = 6822.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.181645 restraints weight = 5387.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.182820 restraints weight = 4616.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.184082 restraints weight = 4234.141| |-----------------------------------------------------------------------------| r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8710 Z= 0.139 Angle : 0.583 8.504 11997 Z= 0.312 Chirality : 0.042 0.163 1310 Planarity : 0.004 0.044 1382 Dihedral : 16.579 75.698 1369 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.13 % Favored : 95.77 % Rotamer: Outliers : 1.56 % Allowed : 13.53 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.28), residues: 921 helix: 1.40 (0.31), residues: 308 sheet: -1.40 (0.42), residues: 145 loop : -0.84 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.015 0.001 TYR B 354 PHE 0.014 0.002 PHE A 160 TRP 0.011 0.001 TRP A 402 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 8710) covalent geometry : angle 0.58349 / 0.31 (11997) hydrogen bonds : bond 0.03480 / 2.24 ( 313) hydrogen bonds : angle 4.78579 / 3.12 ( 828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 281 LYS cc_start: 0.5339 (mmtt) cc_final: 0.5073 (mmtt) REVERT: B 180 ILE cc_start: 0.7420 (mm) cc_final: 0.6977 (tt) REVERT: B 409 THR cc_start: 0.7133 (m) cc_final: 0.6758 (p) outliers start: 13 outliers final: 10 residues processed: 118 average time/residue: 0.0818 time to fit residues: 14.1018 Evaluate side-chains 113 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 40.0000 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.219523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.173752 restraints weight = 9881.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.177268 restraints weight = 6914.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.179140 restraints weight = 5466.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.180914 restraints weight = 4754.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.181650 restraints weight = 4337.807| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8710 Z= 0.157 Angle : 0.612 7.904 11997 Z= 0.324 Chirality : 0.043 0.168 1310 Planarity : 0.004 0.042 1382 Dihedral : 16.616 75.843 1369 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 2.04 % Allowed : 14.49 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.28), residues: 921 helix: 1.29 (0.31), residues: 303 sheet: -1.45 (0.42), residues: 139 loop : -1.02 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 356 TYR 0.016 0.002 TYR B 354 PHE 0.015 0.002 PHE B 130 TRP 0.013 0.001 TRP B 398 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 8710) covalent geometry : angle 0.61232 / 0.32 (11997) hydrogen bonds : bond 0.03690 / 2.40 ( 313) hydrogen bonds : angle 4.90293 / 3.18 ( 828) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 228 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7282 (tt) REVERT: A 281 LYS cc_start: 0.5377 (mmtt) cc_final: 0.5163 (mmtt) REVERT: B 180 ILE cc_start: 0.7498 (mm) cc_final: 0.7057 (tt) outliers start: 17 outliers final: 12 residues processed: 121 average time/residue: 0.0906 time to fit residues: 15.6013 Evaluate side-chains 118 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 13 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 73 optimal weight: 0.0570 overall best weight: 1.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.222210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.174698 restraints weight = 9959.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.179655 restraints weight = 6047.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.182902 restraints weight = 4403.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.184611 restraints weight = 3613.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.186175 restraints weight = 3225.669| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8710 Z= 0.121 Angle : 0.568 8.189 11997 Z= 0.302 Chirality : 0.042 0.148 1310 Planarity : 0.004 0.042 1382 Dihedral : 16.431 74.546 1369 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 2.16 % Allowed : 15.69 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.28), residues: 921 helix: 1.40 (0.31), residues: 309 sheet: -1.36 (0.43), residues: 136 loop : -0.88 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 448 TYR 0.014 0.001 TYR B 354 PHE 0.011 0.001 PHE A 171 TRP 0.012 0.001 TRP B 398 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 8710) covalent geometry : angle 0.56760 / 0.30 (11997) hydrogen bonds : bond 0.03305 / 2.14 ( 313) hydrogen bonds : angle 4.77317 / 3.11 ( 828) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 281 LYS cc_start: 0.5388 (mmtt) cc_final: 0.5124 (mmtt) REVERT: A 357 MET cc_start: 0.5798 (ttt) cc_final: 0.5233 (tpp) REVERT: B 180 ILE cc_start: 0.7482 (mm) cc_final: 0.7070 (tt) outliers start: 18 outliers final: 13 residues processed: 126 average time/residue: 0.0880 time to fit residues: 15.7099 Evaluate side-chains 118 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 40.0000 chunk 50 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 0.0570 chunk 70 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 overall best weight: 2.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN B 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.223845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.178692 restraints weight = 9979.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.183349 restraints weight = 6168.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.186442 restraints weight = 4544.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.188497 restraints weight = 3747.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.189582 restraints weight = 3320.298| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8710 Z= 0.125 Angle : 0.573 7.482 11997 Z= 0.303 Chirality : 0.042 0.237 1310 Planarity : 0.004 0.041 1382 Dihedral : 16.372 74.776 1369 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.13 % Favored : 95.77 % Rotamer: Outliers : 2.16 % Allowed : 16.05 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.28), residues: 921 helix: 1.51 (0.31), residues: 303 sheet: -1.23 (0.44), residues: 134 loop : -0.89 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.015 0.001 TYR B 354 PHE 0.010 0.001 PHE B 130 TRP 0.013 0.001 TRP B 398 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 8710) covalent geometry : angle 0.57295 / 0.30 (11997) hydrogen bonds : bond 0.03298 / 2.13 ( 313) hydrogen bonds : angle 4.75421 / 3.10 ( 828) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 102 LYS cc_start: 0.5560 (tmtt) cc_final: 0.5181 (tmtt) REVERT: A 281 LYS cc_start: 0.5430 (mmtt) cc_final: 0.5137 (mmtt) REVERT: A 357 MET cc_start: 0.5801 (ttt) cc_final: 0.5401 (tpp) REVERT: B 180 ILE cc_start: 0.7523 (mm) cc_final: 0.7146 (tt) REVERT: B 184 MET cc_start: 0.7178 (mmt) cc_final: 0.6909 (mmt) outliers start: 18 outliers final: 15 residues processed: 119 average time/residue: 0.0836 time to fit residues: 14.1501 Evaluate side-chains 117 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 0.0270 chunk 45 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.219463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.175638 restraints weight = 9929.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.175747 restraints weight = 7298.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.177354 restraints weight = 6401.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.179572 restraints weight = 5320.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.179530 restraints weight = 4839.240| |-----------------------------------------------------------------------------| r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8710 Z= 0.152 Angle : 0.613 7.747 11997 Z= 0.321 Chirality : 0.043 0.181 1310 Planarity : 0.004 0.040 1382 Dihedral : 16.461 75.135 1369 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.21 % Favored : 94.68 % Rotamer: Outliers : 2.04 % Allowed : 16.53 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.28), residues: 921 helix: 1.36 (0.31), residues: 303 sheet: -1.29 (0.44), residues: 134 loop : -0.95 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.017 0.002 TYR B 354 PHE 0.014 0.002 PHE B 130 TRP 0.016 0.002 TRP B 398 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 8710) covalent geometry : angle 0.61252 / 0.32 (11997) hydrogen bonds : bond 0.03621 / 2.33 ( 313) hydrogen bonds : angle 4.88015 / 3.18 ( 828) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 102 LYS cc_start: 0.5671 (tmtt) cc_final: 0.5249 (tmtt) REVERT: A 228 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7260 (tt) REVERT: A 357 MET cc_start: 0.5837 (ttt) cc_final: 0.5502 (tpp) REVERT: B 180 ILE cc_start: 0.7556 (mm) cc_final: 0.7164 (tt) outliers start: 17 outliers final: 15 residues processed: 114 average time/residue: 0.0761 time to fit residues: 12.3578 Evaluate side-chains 117 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 42 optimal weight: 50.0000 chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 30.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.219141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.175796 restraints weight = 9899.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.175331 restraints weight = 7336.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.177410 restraints weight = 6461.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.180685 restraints weight = 5220.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.180271 restraints weight = 4604.832| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8710 Z= 0.148 Angle : 0.604 7.656 11997 Z= 0.317 Chirality : 0.043 0.184 1310 Planarity : 0.004 0.041 1382 Dihedral : 16.443 75.571 1369 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.21 % Favored : 94.68 % Rotamer: Outliers : 2.04 % Allowed : 16.41 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.28), residues: 921 helix: 1.40 (0.31), residues: 302 sheet: -1.36 (0.43), residues: 139 loop : -1.02 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.015 0.002 TYR B 354 PHE 0.014 0.002 PHE B 130 TRP 0.017 0.001 TRP B 398 HIS 0.003 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 8710) covalent geometry : angle 0.60402 / 0.32 (11997) hydrogen bonds : bond 0.03562 / 2.31 ( 313) hydrogen bonds : angle 4.88710 / 3.19 ( 828) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 102 LYS cc_start: 0.5596 (tmtt) cc_final: 0.5185 (tmtt) REVERT: A 228 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7255 (tt) REVERT: A 281 LYS cc_start: 0.5307 (mmtt) cc_final: 0.5058 (mmtt) REVERT: A 357 MET cc_start: 0.5770 (ttt) cc_final: 0.5456 (tpp) REVERT: A 466 VAL cc_start: 0.4876 (t) cc_final: 0.4650 (t) REVERT: B 180 ILE cc_start: 0.7539 (mm) cc_final: 0.7149 (tt) REVERT: B 203 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6065 (pt0) outliers start: 17 outliers final: 15 residues processed: 119 average time/residue: 0.0818 time to fit residues: 13.9310 Evaluate side-chains 120 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 75 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 50.0000 chunk 76 optimal weight: 8.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.216774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.173416 restraints weight = 9961.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.173007 restraints weight = 7167.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.174801 restraints weight = 6516.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.176478 restraints weight = 5318.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.176638 restraints weight = 4988.170| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8710 Z= 0.195 Angle : 0.682 13.242 11997 Z= 0.353 Chirality : 0.045 0.201 1310 Planarity : 0.005 0.041 1382 Dihedral : 16.604 77.204 1369 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.41 % Favored : 93.49 % Rotamer: Outliers : 2.28 % Allowed : 16.89 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.28), residues: 921 helix: 1.12 (0.30), residues: 301 sheet: -1.51 (0.43), residues: 139 loop : -1.12 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 448 TYR 0.018 0.002 TYR B 354 PHE 0.019 0.003 PHE B 130 TRP 0.017 0.002 TRP B 398 HIS 0.006 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 ( 8710) covalent geometry : angle 0.68165 / 0.35 (11997) hydrogen bonds : bond 0.04116 / 2.64 ( 313) hydrogen bonds : angle 5.13042 / 3.35 ( 828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1410.37 seconds wall clock time: 25 minutes 11.42 seconds (1511.42 seconds total)