Starting phenix.real_space_refine on Sat Aug 23 02:56:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jek_36191/08_2025/8jek_36191.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jek_36191/08_2025/8jek_36191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jek_36191/08_2025/8jek_36191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jek_36191/08_2025/8jek_36191.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jek_36191/08_2025/8jek_36191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jek_36191/08_2025/8jek_36191.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.047 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: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 P 2 5.49 5 S 46 5.16 5 C 5440 2.51 5 N 1490 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s 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: 8623 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4167 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 503} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 387} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 186 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1} Unresolved non-hydrogen planarities: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1767 SG CYS A 226 51.827 64.206 39.994 1.00 27.34 S ATOM 1738 SG CYS A 222 50.728 68.892 44.226 1.00 28.24 S ATOM 1698 SG CYS A 216 52.433 63.595 46.715 1.00 34.01 S Time building chain proxies: 2.06, per 1000 atoms: 0.24 Number of scatterers: 8623 At special positions: 0 Unit cell: (104.4, 108.75, 77.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 46 16.00 P 2 15.00 O 1639 8.00 N 1490 7.00 C 5440 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 262.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 8 sheets defined 41.4% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.923A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.924A pdb=" N THR A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 233 through 244 removed outlier: 4.173A pdb=" N ALA A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.588A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 387 through 401 removed outlier: 3.651A pdb=" N LEU A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 462 removed outlier: 4.194A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.523A pdb=" N THR A 513 " --> pdb=" O THR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 541 Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 68 through 83 Processing helix chain 'B' and resid 85 through 101 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.548A pdb=" N SER B 172 " --> pdb=" O TYR B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 Processing helix chain 'C' and resid 51 through 56 removed outlier: 4.313A pdb=" N CYS C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS C 56 " --> pdb=" O CYS C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 56' Processing helix chain 'C' and resid 95 through 106 removed outlier: 3.518A pdb=" N GLY C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.915A pdb=" N ARG C 125 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 141 Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.685A pdb=" N TYR C 219 " --> pdb=" O GLN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 256 Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'C' and resid 275 through 278 Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 317 through 324 removed outlier: 3.752A pdb=" N SER C 322 " --> pdb=" O ASN C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 431 through 440 Processing helix chain 'C' and resid 445 through 451 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.657A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP A 9 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL A 286 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 11 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU A 258 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 268 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA A 256 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE A 270 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL A 254 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.657A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP A 9 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL A 286 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 11 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N PHE A 507 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE A 285 " --> pdb=" O PHE A 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.429A pdb=" N ILE A 87 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N HIS A 433 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 157 Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.457A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY A 328 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N MET A 469 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER A 330 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE A 467 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AA7, first strand: chain 'C' and resid 223 through 225 Processing sheet with id=AA8, first strand: chain 'C' and resid 384 through 388 319 hydrogen bonds defined for protein. 867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 8764 1.76 - 2.31: 90 2.31 - 2.85: 0 2.85 - 3.39: 0 3.39 - 3.94: 3 Bond restraints: 8857 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.935 -1.635 2.00e-02 2.50e+03 6.69e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.818 -1.585 2.00e-02 2.50e+03 6.28e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.789 -1.531 2.00e-02 2.50e+03 5.86e+03 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.329 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C2D HEC C 503 " pdb=" C3D HEC C 503 " ideal model delta sigma weight residual 1.544 1.333 0.211 2.00e-02 2.50e+03 1.11e+02 ... (remaining 8852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.46: 12088 9.46 - 18.93: 6 18.93 - 28.39: 0 28.39 - 37.85: 8 37.85 - 47.31: 2 Bond angle restraints: 12104 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 67.44 47.31 3.00e+00 1.11e-01 2.49e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 67.16 45.43 3.00e+00 1.11e-01 2.29e+02 angle pdb=" S1 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " ideal model delta sigma weight residual 103.25 68.87 34.38 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 103.26 69.18 34.08 3.00e+00 1.11e-01 1.29e+02 angle pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 71.75 39.22 32.53 3.00e+00 1.11e-01 1.18e+02 ... (remaining 12099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 5052 34.62 - 69.24: 170 69.24 - 103.86: 18 103.86 - 138.48: 0 138.48 - 173.09: 1 Dihedral angle restraints: 5241 sinusoidal: 2089 harmonic: 3152 Sorted by residual: dihedral pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta harmonic sigma weight residual -180.00 -119.72 -60.28 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" C37 U10 C 504 " pdb=" C38 U10 C 504 " pdb=" C39 U10 C 504 " pdb=" C41 U10 C 504 " ideal model delta sinusoidal sigma weight residual -5.63 167.47 -173.09 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C2C HEC C 502 " pdb=" C3C HEC C 502 " pdb=" CAC HEC C 502 " pdb=" CBC HEC C 502 " ideal model delta sinusoidal sigma weight residual -120.00 -38.15 -81.85 2 1.00e+01 1.00e-02 4.70e+01 ... (remaining 5238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.462: 1276 3.462 - 6.924: 0 6.924 - 10.386: 0 10.386 - 13.848: 0 13.848 - 17.310: 1 Chirality restraints: 1277 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -6.54 17.31 2.00e-01 2.50e+01 7.49e+03 chirality pdb=" CB ILE C 393 " pdb=" CA ILE C 393 " pdb=" CG1 ILE C 393 " pdb=" CG2 ILE C 393 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" C3' FAD A 601 " pdb=" C2' FAD A 601 " pdb=" C4' FAD A 601 " pdb=" O3' FAD A 601 " both_signs ideal model delta sigma weight residual False -2.55 -2.34 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1274 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 C 504 " -0.001 2.00e-02 2.50e+03 9.06e-02 1.44e+02 pdb=" C1M U10 C 504 " 0.063 2.00e-02 2.50e+03 pdb=" C2 U10 C 504 " 0.028 2.00e-02 2.50e+03 pdb=" C3 U10 C 504 " -0.133 2.00e-02 2.50e+03 pdb=" C4 U10 C 504 " 0.144 2.00e-02 2.50e+03 pdb=" C5 U10 C 504 " 0.015 2.00e-02 2.50e+03 pdb=" C6 U10 C 504 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEC C 501 " -0.033 2.00e-02 2.50e+03 6.99e-02 4.88e+01 pdb=" CGD HEC C 501 " 0.121 2.00e-02 2.50e+03 pdb=" O1D HEC C 501 " -0.043 2.00e-02 2.50e+03 pdb=" O2D HEC C 501 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 80 " -0.101 5.00e-02 4.00e+02 1.56e-01 3.91e+01 pdb=" N PRO A 81 " 0.271 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.081 5.00e-02 4.00e+02 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 450 2.72 - 3.27: 8576 3.27 - 3.81: 15262 3.81 - 4.36: 19757 4.36 - 4.90: 32516 Nonbonded interactions: 76561 Sorted by model distance: nonbonded pdb=" O ALA C 397 " pdb=" OG SER C 402 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR A 118 " pdb=" O SER A 517 " model vdw 2.189 3.040 nonbonded pdb=" O ARG A 358 " pdb=" OH TYR A 443 " model vdw 2.195 3.040 nonbonded pdb=" OG SER C 354 " pdb=" OD1 ASP C 356 " model vdw 2.219 3.040 nonbonded pdb=" S4 F3S A 602 " pdb="FE4 F3S A 602 " model vdw 2.257 2.688 ... (remaining 76556 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 0.020 Process input model: 10.670 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.031 1.635 8871 Z= 1.518 Angle : 1.354 47.314 12113 Z= 0.518 Chirality : 0.487 17.310 1277 Planarity : 0.008 0.156 1572 Dihedral : 17.134 173.095 3229 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.69 % Allowed : 13.21 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: 0.19 (0.25), residues: 1083 helix: 1.47 (0.28), residues: 363 sheet: 0.37 (0.64), residues: 72 loop : -0.70 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 125 TYR 0.014 0.001 TYR A 79 PHE 0.017 0.001 PHE A 270 TRP 0.017 0.001 TRP A 111 HIS 0.006 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.03056 ( 8857) covalent geometry : angle 1.33901 (12104) hydrogen bonds : bond 0.14473 ( 316) hydrogen bonds : angle 6.72559 ( 867) metal coordination : bond 0.00123 ( 3) metal coordination : angle 7.42377 ( 9) Misc. bond : bond 0.03533 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.263 Fit side-chains REVERT: A 505 ASN cc_start: 0.7804 (t0) cc_final: 0.7253 (t0) REVERT: C 315 TYR cc_start: 0.6711 (OUTLIER) cc_final: 0.5098 (p90) outliers start: 15 outliers final: 13 residues processed: 117 average time/residue: 0.4680 time to fit residues: 59.2450 Evaluate side-chains 118 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 445 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0070 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.105499 restraints weight = 9034.962| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.55 r_work: 0.3056 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.184 8871 Z= 0.214 Angle : 1.497 71.001 12113 Z= 0.487 Chirality : 0.101 3.235 1277 Planarity : 0.006 0.112 1572 Dihedral : 12.116 155.029 1318 Min Nonbonded Distance : 1.548 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.60 % Allowed : 11.63 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.40 (0.26), residues: 1083 helix: 1.62 (0.27), residues: 386 sheet: 0.40 (0.65), residues: 72 loop : -0.63 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.016 0.001 TYR A 79 PHE 0.014 0.001 PHE A 80 TRP 0.011 0.001 TRP A 111 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 8857) covalent geometry : angle 1.31218 (12104) hydrogen bonds : bond 0.03937 ( 316) hydrogen bonds : angle 5.23012 ( 867) metal coordination : bond 0.01058 ( 3) metal coordination : angle 26.47359 ( 9) Misc. bond : bond 0.05714 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8733 (m110) cc_final: 0.8481 (m110) REVERT: A 478 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.6917 (p-80) REVERT: C 143 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7021 (pttp) outliers start: 23 outliers final: 9 residues processed: 121 average time/residue: 0.4343 time to fit residues: 56.7918 Evaluate side-chains 116 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** C 124 ASN ** 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 = 0.3418 r_free = 0.3418 target = 0.129327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.100712 restraints weight = 9142.444| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.53 r_work: 0.2983 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.213 8871 Z= 0.233 Angle : 1.508 83.090 12113 Z= 0.445 Chirality : 0.062 1.327 1277 Planarity : 0.006 0.100 1572 Dihedral : 12.182 149.953 1309 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.08 % Favored : 94.83 % Rotamer: Outliers : 3.05 % Allowed : 12.87 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.23 (0.26), residues: 1083 helix: 1.47 (0.27), residues: 385 sheet: 0.35 (0.64), residues: 73 loop : -0.73 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.021 0.002 TYR A 79 PHE 0.019 0.002 PHE A 80 TRP 0.010 0.002 TRP A 173 HIS 0.007 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 8857) covalent geometry : angle 1.10693 (12104) hydrogen bonds : bond 0.04650 ( 316) hydrogen bonds : angle 5.30451 ( 867) metal coordination : bond 0.01107 ( 3) metal coordination : angle 37.61161 ( 9) Misc. bond : bond 0.07575 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 478 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.7199 (p-80) REVERT: A 539 ASN cc_start: 0.8385 (t0) cc_final: 0.8038 (t0) REVERT: B 55 MET cc_start: 0.8474 (mmm) cc_final: 0.8257 (mmm) REVERT: C 143 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.6968 (pttp) outliers start: 27 outliers final: 13 residues processed: 121 average time/residue: 0.4721 time to fit residues: 61.5737 Evaluate side-chains 122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 505 ASN C 326 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.135263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109699 restraints weight = 8903.570| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.19 r_work: 0.3093 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 8871 Z= 0.151 Angle : 1.387 82.587 12113 Z= 0.411 Chirality : 0.061 1.450 1277 Planarity : 0.005 0.098 1572 Dihedral : 11.758 144.786 1308 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 2.48 % Allowed : 14.00 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.41 (0.26), residues: 1083 helix: 1.55 (0.27), residues: 393 sheet: 0.32 (0.64), residues: 73 loop : -0.58 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 323 TYR 0.017 0.001 TYR A 79 PHE 0.015 0.001 PHE A 270 TRP 0.008 0.001 TRP A 111 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8857) covalent geometry : angle 1.04480 (12104) hydrogen bonds : bond 0.03773 ( 316) hydrogen bonds : angle 5.06284 ( 867) metal coordination : bond 0.00466 ( 3) metal coordination : angle 33.45699 ( 9) Misc. bond : bond 0.06979 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8856 (m110) cc_final: 0.8624 (m110) REVERT: A 478 HIS cc_start: 0.7611 (OUTLIER) cc_final: 0.7176 (p-80) REVERT: A 539 ASN cc_start: 0.8504 (t0) cc_final: 0.8185 (t0) REVERT: C 143 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7154 (pttp) outliers start: 22 outliers final: 12 residues processed: 118 average time/residue: 0.4302 time to fit residues: 54.8260 Evaluate side-chains 118 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 5 optimal weight: 0.0370 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.135382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.109966 restraints weight = 8910.028| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.19 r_work: 0.3108 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 8871 Z= 0.145 Angle : 1.381 82.556 12113 Z= 0.406 Chirality : 0.061 1.457 1277 Planarity : 0.005 0.099 1572 Dihedral : 11.505 137.093 1308 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.60 % Allowed : 14.33 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.52 (0.26), residues: 1083 helix: 1.67 (0.27), residues: 393 sheet: 0.44 (0.65), residues: 71 loop : -0.53 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.016 0.001 TYR A 79 PHE 0.015 0.001 PHE A 270 TRP 0.007 0.001 TRP A 111 HIS 0.004 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8857) covalent geometry : angle 1.03508 (12104) hydrogen bonds : bond 0.03566 ( 316) hydrogen bonds : angle 4.94995 ( 867) metal coordination : bond 0.00396 ( 3) metal coordination : angle 33.57348 ( 9) Misc. bond : bond 0.06177 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8886 (m110) cc_final: 0.8672 (m110) REVERT: A 478 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.7152 (p-80) REVERT: A 539 ASN cc_start: 0.8492 (t0) cc_final: 0.8170 (t0) REVERT: B 112 MET cc_start: 0.8329 (ttp) cc_final: 0.8125 (ttp) REVERT: C 143 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7142 (pttp) outliers start: 23 outliers final: 13 residues processed: 117 average time/residue: 0.4182 time to fit residues: 52.9408 Evaluate side-chains 117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 85 optimal weight: 0.0970 chunk 92 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.135469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.109862 restraints weight = 8820.992| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.18 r_work: 0.3077 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 8871 Z= 0.174 Angle : 1.400 82.207 12113 Z= 0.418 Chirality : 0.062 1.466 1277 Planarity : 0.005 0.093 1572 Dihedral : 11.524 131.028 1308 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 3.27 % Allowed : 13.54 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.44 (0.26), residues: 1083 helix: 1.57 (0.27), residues: 393 sheet: 0.44 (0.64), residues: 72 loop : -0.57 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.019 0.001 TYR A 79 PHE 0.017 0.001 PHE A 270 TRP 0.009 0.001 TRP B 128 HIS 0.005 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8857) covalent geometry : angle 1.05720 (12104) hydrogen bonds : bond 0.03941 ( 316) hydrogen bonds : angle 5.03238 ( 867) metal coordination : bond 0.00458 ( 3) metal coordination : angle 33.67826 ( 9) Misc. bond : bond 0.07224 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8870 (m110) cc_final: 0.8626 (m110) REVERT: A 478 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.7222 (p-80) REVERT: A 539 ASN cc_start: 0.8507 (t0) cc_final: 0.8186 (t0) REVERT: B 112 MET cc_start: 0.8348 (ttp) cc_final: 0.8137 (ttp) REVERT: B 126 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7226 (mtp180) REVERT: C 118 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.6220 (tpt) REVERT: C 143 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7116 (pttp) outliers start: 29 outliers final: 17 residues processed: 118 average time/residue: 0.4579 time to fit residues: 58.4811 Evaluate side-chains 122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 0.0570 overall best weight: 0.8900 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.135822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.110212 restraints weight = 8865.573| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.19 r_work: 0.3090 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.195 8871 Z= 0.161 Angle : 1.393 82.082 12113 Z= 0.414 Chirality : 0.062 1.476 1277 Planarity : 0.005 0.105 1572 Dihedral : 11.397 125.346 1308 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.82 % Allowed : 14.11 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.50 (0.26), residues: 1083 helix: 1.61 (0.27), residues: 393 sheet: 0.47 (0.65), residues: 71 loop : -0.53 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.016 0.001 TYR A 79 PHE 0.017 0.001 PHE A 270 TRP 0.007 0.001 TRP B 128 HIS 0.004 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8857) covalent geometry : angle 1.04771 (12104) hydrogen bonds : bond 0.03732 ( 316) hydrogen bonds : angle 4.98962 ( 867) metal coordination : bond 0.00402 ( 3) metal coordination : angle 33.69097 ( 9) Misc. bond : bond 0.07154 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8916 (m110) cc_final: 0.8693 (m110) REVERT: A 478 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7185 (p-80) REVERT: A 539 ASN cc_start: 0.8510 (t0) cc_final: 0.8185 (t0) REVERT: B 112 MET cc_start: 0.8337 (ttp) cc_final: 0.8117 (ttp) REVERT: B 126 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7145 (mtp180) REVERT: B 183 PHE cc_start: 0.6894 (OUTLIER) cc_final: 0.5527 (p90) REVERT: C 118 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.6215 (tpt) REVERT: C 143 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7123 (pttp) outliers start: 25 outliers final: 17 residues processed: 115 average time/residue: 0.4887 time to fit residues: 60.6677 Evaluate side-chains 124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 41 optimal weight: 0.0870 chunk 60 optimal weight: 0.0770 chunk 72 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.138288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.113071 restraints weight = 8825.103| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.18 r_work: 0.3115 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 8871 Z= 0.142 Angle : 1.377 82.366 12113 Z= 0.405 Chirality : 0.061 1.469 1277 Planarity : 0.005 0.106 1572 Dihedral : 11.127 115.755 1308 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.60 % Allowed : 14.22 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.61 (0.26), residues: 1083 helix: 1.72 (0.27), residues: 393 sheet: 0.51 (0.65), residues: 71 loop : -0.47 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.015 0.001 TYR A 79 PHE 0.015 0.001 PHE A 270 TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8857) covalent geometry : angle 1.03547 (12104) hydrogen bonds : bond 0.03406 ( 316) hydrogen bonds : angle 4.88323 ( 867) metal coordination : bond 0.00353 ( 3) metal coordination : angle 33.31969 ( 9) Misc. bond : bond 0.06312 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.7076 (p-80) REVERT: A 539 ASN cc_start: 0.8503 (t0) cc_final: 0.8189 (t0) REVERT: B 112 MET cc_start: 0.8327 (ttp) cc_final: 0.8110 (ttp) REVERT: B 126 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7153 (mtp85) REVERT: C 118 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.6231 (tpt) REVERT: C 143 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7111 (pttp) REVERT: C 315 TYR cc_start: 0.6835 (OUTLIER) cc_final: 0.5941 (p90) outliers start: 23 outliers final: 15 residues processed: 113 average time/residue: 0.4169 time to fit residues: 50.9737 Evaluate side-chains 118 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 403 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 8 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.136319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110794 restraints weight = 8820.567| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.19 r_work: 0.3071 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.213 8871 Z= 0.162 Angle : 1.397 82.161 12113 Z= 0.415 Chirality : 0.062 1.474 1277 Planarity : 0.005 0.104 1572 Dihedral : 11.154 112.072 1308 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.60 % Allowed : 14.67 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.56 (0.26), residues: 1083 helix: 1.69 (0.27), residues: 393 sheet: 0.52 (0.65), residues: 71 loop : -0.51 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.018 0.001 TYR A 79 PHE 0.018 0.001 PHE A 270 TRP 0.008 0.001 TRP B 128 HIS 0.004 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8857) covalent geometry : angle 1.05480 (12104) hydrogen bonds : bond 0.03695 ( 316) hydrogen bonds : angle 4.95368 ( 867) metal coordination : bond 0.00429 ( 3) metal coordination : angle 33.64825 ( 9) Misc. bond : bond 0.07405 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 HIS cc_start: 0.7633 (OUTLIER) cc_final: 0.7196 (p-80) REVERT: A 539 ASN cc_start: 0.8504 (t0) cc_final: 0.8182 (t0) REVERT: B 112 MET cc_start: 0.8341 (ttp) cc_final: 0.8121 (ttp) REVERT: B 126 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7144 (mtp180) REVERT: B 183 PHE cc_start: 0.6863 (OUTLIER) cc_final: 0.5281 (p90) REVERT: C 118 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.6203 (tpt) REVERT: C 143 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7098 (pttp) outliers start: 23 outliers final: 16 residues processed: 114 average time/residue: 0.5440 time to fit residues: 66.6733 Evaluate side-chains 123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 403 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 85 optimal weight: 0.0980 chunk 99 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.137957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.112659 restraints weight = 8808.329| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.18 r_work: 0.3112 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 8871 Z= 0.149 Angle : 1.386 82.290 12113 Z= 0.409 Chirality : 0.061 1.468 1277 Planarity : 0.005 0.101 1572 Dihedral : 11.013 106.184 1308 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.14 % Allowed : 15.69 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.61 (0.26), residues: 1083 helix: 1.74 (0.27), residues: 393 sheet: 0.56 (0.65), residues: 71 loop : -0.48 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.015 0.001 TYR A 79 PHE 0.016 0.001 PHE A 270 TRP 0.007 0.001 TRP A 111 HIS 0.004 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8857) covalent geometry : angle 1.04367 (12104) hydrogen bonds : bond 0.03485 ( 316) hydrogen bonds : angle 4.89694 ( 867) metal coordination : bond 0.00394 ( 3) metal coordination : angle 33.48580 ( 9) Misc. bond : bond 0.06789 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.7071 (p-80) REVERT: A 539 ASN cc_start: 0.8505 (t0) cc_final: 0.8188 (t0) REVERT: B 112 MET cc_start: 0.8327 (ttp) cc_final: 0.8110 (ttp) REVERT: B 126 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7134 (mtp180) REVERT: C 118 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.6228 (tpt) REVERT: C 143 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7051 (pttp) outliers start: 19 outliers final: 15 residues processed: 110 average time/residue: 0.4844 time to fit residues: 57.3879 Evaluate side-chains 118 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 59 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 50 optimal weight: 0.0170 chunk 63 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.138651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.113329 restraints weight = 8821.590| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.19 r_work: 0.3129 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 8871 Z= 0.142 Angle : 1.377 82.313 12113 Z= 0.405 Chirality : 0.060 1.471 1277 Planarity : 0.005 0.099 1572 Dihedral : 10.967 99.671 1306 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.03 % Allowed : 15.58 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.68 (0.26), residues: 1083 helix: 1.81 (0.27), residues: 393 sheet: 0.55 (0.65), residues: 71 loop : -0.45 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.015 0.001 TYR A 79 PHE 0.015 0.001 PHE A 270 TRP 0.008 0.001 TRP A 173 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8857) covalent geometry : angle 1.03740 (12104) hydrogen bonds : bond 0.03340 ( 316) hydrogen bonds : angle 4.81862 ( 867) metal coordination : bond 0.00364 ( 3) metal coordination : angle 33.24430 ( 9) Misc. bond : bond 0.07053 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2697.25 seconds wall clock time: 46 minutes 46.53 seconds (2806.53 seconds total)