Starting phenix.real_space_refine on Mon May 12 19:40:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jek_36191/05_2025/8jek_36191.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jek_36191/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jek_36191/05_2025/8jek_36191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jek_36191/05_2025/8jek_36191.map" model { file = "/net/cci-nas-00/data/ceres_data/8jek_36191/05_2025/8jek_36191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jek_36191/05_2025/8jek_36191.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.75, per 1000 atoms: 0.67 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: 2.52 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.92 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: 2.31 Time building geometry restraints manager: 2.85 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.930 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.940 ------------------------------------------------------------------------------- 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 : 7.68 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.017 0.001 TRP A 111 HIS 0.006 0.001 HIS A 110 PHE 0.017 0.001 PHE A 270 TYR 0.014 0.001 TYR A 79 ARG 0.002 0.000 ARG C 125 Details of bonding type rmsd hydrogen bonds : bond 0.14473 ( 316) hydrogen bonds : angle 6.72559 ( 867) metal coordination : bond 0.00123 ( 3) metal coordination : angle 7.42377 ( 9) covalent geometry : bond 0.03056 ( 8857) covalent geometry : angle 1.33901 (12104) 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 : 1.045 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: 1.0397 time to fit residues: 131.6674 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 : 0.899 ------------------------------------------------------------------------------- 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 91 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.132034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.103337 restraints weight = 9006.404| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.55 r_work: 0.2998 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 8871 Z= 0.213 Angle : 1.536 68.807 12113 Z= 0.495 Chirality : 0.099 3.152 1277 Planarity : 0.006 0.111 1572 Dihedral : 12.304 153.489 1318 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 2.71 % Allowed : 11.74 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1083 helix: 1.51 (0.27), residues: 387 sheet: 0.38 (0.64), residues: 73 loop : -0.67 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 111 HIS 0.004 0.001 HIS A 76 PHE 0.015 0.001 PHE A 270 TYR 0.016 0.001 TYR A 79 ARG 0.004 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 316) hydrogen bonds : angle 5.27072 ( 867) metal coordination : bond 0.00707 ( 3) metal coordination : angle 28.67865 ( 9) covalent geometry : bond 0.00468 ( 8857) covalent geometry : angle 1.32280 (12104) Misc. bond : bond 0.05880 ( 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 135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8719 (m110) cc_final: 0.8427 (m110) REVERT: A 478 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.7011 (p-80) REVERT: C 135 TYR cc_start: 0.8339 (t80) cc_final: 0.8083 (t80) REVERT: C 143 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.6982 (pttp) outliers start: 24 outliers final: 10 residues processed: 121 average time/residue: 0.9596 time to fit residues: 126.0962 Evaluate side-chains 117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN C 326 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.127413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.098615 restraints weight = 9309.643| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.54 r_work: 0.2973 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.234 8871 Z= 0.264 Angle : 1.500 83.214 12113 Z= 0.460 Chirality : 0.064 1.356 1277 Planarity : 0.006 0.105 1572 Dihedral : 12.325 149.856 1309 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.64 % Rotamer: Outliers : 2.93 % Allowed : 13.32 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 2.99 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1083 helix: 1.27 (0.27), residues: 385 sheet: 0.08 (0.63), residues: 76 loop : -0.79 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 173 HIS 0.006 0.001 HIS C 200 PHE 0.022 0.002 PHE A 80 TYR 0.020 0.002 TYR A 79 ARG 0.002 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.05021 ( 316) hydrogen bonds : angle 5.42023 ( 867) metal coordination : bond 0.01220 ( 3) metal coordination : angle 36.21730 ( 9) covalent geometry : bond 0.00619 ( 8857) covalent geometry : angle 1.12926 (12104) Misc. bond : bond 0.08656 ( 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 136 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 478 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.7297 (p-80) REVERT: A 539 ASN cc_start: 0.8424 (t0) cc_final: 0.8076 (t0) REVERT: C 135 TYR cc_start: 0.8382 (t80) cc_final: 0.8163 (t80) REVERT: C 143 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7063 (pttp) outliers start: 26 outliers final: 15 residues processed: 123 average time/residue: 1.0578 time to fit residues: 140.3601 Evaluate side-chains 125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 107 ILE 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 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 61 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 chunk 70 optimal weight: 0.0770 chunk 103 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.135871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.110519 restraints weight = 8802.372| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.20 r_work: 0.3106 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 8871 Z= 0.140 Angle : 1.380 83.153 12113 Z= 0.407 Chirality : 0.060 1.427 1277 Planarity : 0.005 0.097 1572 Dihedral : 11.627 141.929 1308 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.60 % Allowed : 14.00 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1083 helix: 1.64 (0.27), residues: 387 sheet: 0.37 (0.63), residues: 72 loop : -0.63 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 111 HIS 0.004 0.001 HIS A 110 PHE 0.013 0.001 PHE A 270 TYR 0.015 0.001 TYR A 79 ARG 0.002 0.000 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 316) hydrogen bonds : angle 5.01233 ( 867) metal coordination : bond 0.00393 ( 3) metal coordination : angle 33.42671 ( 9) covalent geometry : bond 0.00304 ( 8857) covalent geometry : angle 1.03640 (12104) Misc. bond : bond 0.06560 ( 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 130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8846 (m110) cc_final: 0.8622 (m110) REVERT: A 478 HIS cc_start: 0.7523 (OUTLIER) cc_final: 0.7146 (p-80) REVERT: A 539 ASN cc_start: 0.8508 (t0) cc_final: 0.8194 (t0) REVERT: C 143 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7137 (pttp) REVERT: C 315 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.5400 (p90) outliers start: 23 outliers final: 13 residues processed: 118 average time/residue: 1.0156 time to fit residues: 129.7368 Evaluate side-chains 120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 B residue 176 SER 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 5 optimal weight: 2.9990 chunk 28 optimal weight: 0.0040 chunk 7 optimal weight: 0.9980 chunk 95 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.5750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.137717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.112548 restraints weight = 8732.510| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.18 r_work: 0.3111 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 8871 Z= 0.142 Angle : 1.378 82.581 12113 Z= 0.405 Chirality : 0.060 1.451 1277 Planarity : 0.005 0.098 1572 Dihedral : 11.398 133.200 1308 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.71 % Allowed : 14.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1083 helix: 1.64 (0.27), residues: 393 sheet: 0.44 (0.64), residues: 71 loop : -0.53 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 111 HIS 0.003 0.001 HIS A 76 PHE 0.014 0.001 PHE A 270 TYR 0.017 0.001 TYR A 79 ARG 0.002 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 316) hydrogen bonds : angle 4.95158 ( 867) metal coordination : bond 0.00408 ( 3) metal coordination : angle 33.53940 ( 9) covalent geometry : bond 0.00311 ( 8857) covalent geometry : angle 1.03117 (12104) Misc. bond : bond 0.05418 ( 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 132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8884 (m110) cc_final: 0.8677 (m110) REVERT: A 478 HIS cc_start: 0.7532 (OUTLIER) cc_final: 0.7086 (p-80) REVERT: A 539 ASN cc_start: 0.8493 (t0) cc_final: 0.8180 (t0) REVERT: B 126 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7202 (mtp85) REVERT: C 143 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7150 (pttp) outliers start: 24 outliers final: 14 residues processed: 120 average time/residue: 1.0163 time to fit residues: 131.8389 Evaluate side-chains 122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.134312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.108617 restraints weight = 8696.250| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.17 r_work: 0.3068 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.213 8871 Z= 0.187 Angle : 1.412 82.137 12113 Z= 0.423 Chirality : 0.063 1.466 1277 Planarity : 0.006 0.095 1572 Dihedral : 11.577 131.212 1308 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 3.05 % Allowed : 13.66 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1083 helix: 1.53 (0.27), residues: 393 sheet: 0.45 (0.63), residues: 72 loop : -0.60 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 128 HIS 0.006 0.001 HIS C 200 PHE 0.018 0.002 PHE A 270 TYR 0.020 0.001 TYR A 79 ARG 0.002 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 316) hydrogen bonds : angle 5.07842 ( 867) metal coordination : bond 0.00497 ( 3) metal coordination : angle 34.00242 ( 9) covalent geometry : bond 0.00430 ( 8857) covalent geometry : angle 1.06556 (12104) Misc. bond : bond 0.07478 ( 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 136 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8888 (m110) cc_final: 0.8635 (m110) REVERT: A 478 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.7262 (p-80) REVERT: A 539 ASN cc_start: 0.8508 (t0) cc_final: 0.8184 (t0) REVERT: B 126 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7234 (mtp180) REVERT: B 183 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.5879 (p90) REVERT: C 143 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7123 (pttp) outliers start: 27 outliers final: 14 residues processed: 122 average time/residue: 1.0693 time to fit residues: 141.1551 Evaluate side-chains 124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.135954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.110343 restraints weight = 8783.757| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.19 r_work: 0.3067 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1101 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= 0.159 Angle : 1.393 82.105 12113 Z= 0.414 Chirality : 0.062 1.473 1277 Planarity : 0.005 0.105 1572 Dihedral : 11.353 124.578 1308 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.48 % Allowed : 14.11 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1083 helix: 1.60 (0.27), residues: 393 sheet: 0.49 (0.65), residues: 71 loop : -0.54 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 128 HIS 0.004 0.001 HIS A 76 PHE 0.016 0.001 PHE A 270 TYR 0.016 0.001 TYR A 79 ARG 0.002 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 316) hydrogen bonds : angle 4.99087 ( 867) metal coordination : bond 0.00419 ( 3) metal coordination : angle 33.73797 ( 9) covalent geometry : bond 0.00356 ( 8857) covalent geometry : angle 1.04663 (12104) Misc. bond : bond 0.06953 ( 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: 22 poor density : 106 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8913 (m110) cc_final: 0.8688 (m110) REVERT: A 478 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.7180 (p-80) REVERT: A 539 ASN cc_start: 0.8498 (t0) cc_final: 0.8177 (t0) REVERT: B 126 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7190 (mtp180) REVERT: C 143 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7117 (pttp) outliers start: 22 outliers final: 15 residues processed: 116 average time/residue: 0.9849 time to fit residues: 123.5606 Evaluate side-chains 120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.134427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.108780 restraints weight = 8870.142| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.20 r_work: 0.3070 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.223 8871 Z= 0.178 Angle : 1.413 81.947 12113 Z= 0.423 Chirality : 0.063 1.481 1277 Planarity : 0.006 0.110 1572 Dihedral : 11.384 121.299 1308 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 2.82 % Allowed : 14.22 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1083 helix: 1.56 (0.27), residues: 392 sheet: 0.49 (0.64), residues: 72 loop : -0.58 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.005 0.001 HIS C 200 PHE 0.018 0.001 PHE A 270 TYR 0.020 0.001 TYR A 79 ARG 0.002 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 316) hydrogen bonds : angle 5.04923 ( 867) metal coordination : bond 0.00464 ( 3) metal coordination : angle 34.10968 ( 9) covalent geometry : bond 0.00406 ( 8857) covalent geometry : angle 1.06386 (12104) Misc. bond : bond 0.07827 ( 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 129 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8904 (m110) cc_final: 0.8651 (m110) REVERT: A 478 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.7226 (p-80) REVERT: A 539 ASN cc_start: 0.8500 (t0) cc_final: 0.8179 (t0) REVERT: B 126 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7186 (mtp180) REVERT: B 183 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.5654 (p90) REVERT: C 143 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7086 (pttp) outliers start: 25 outliers final: 17 residues processed: 116 average time/residue: 1.0231 time to fit residues: 128.5865 Evaluate side-chains 124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 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 102 optimal weight: 1.9990 chunk 66 optimal weight: 0.0870 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 67 optimal weight: 0.0970 chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.137090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.111672 restraints weight = 8856.591| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.19 r_work: 0.3108 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.200 8871 Z= 0.147 Angle : 1.385 82.219 12113 Z= 0.409 Chirality : 0.061 1.470 1277 Planarity : 0.005 0.109 1572 Dihedral : 11.075 113.086 1308 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.48 % Allowed : 14.90 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1083 helix: 1.68 (0.27), residues: 393 sheet: 0.52 (0.65), residues: 71 loop : -0.50 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 PHE 0.016 0.001 PHE A 270 TYR 0.014 0.001 TYR A 79 ARG 0.002 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 316) hydrogen bonds : angle 4.91601 ( 867) metal coordination : bond 0.00378 ( 3) metal coordination : angle 33.49211 ( 9) covalent geometry : bond 0.00324 ( 8857) covalent geometry : angle 1.04192 (12104) Misc. bond : bond 0.06982 ( 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 124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: A 171 ASN cc_start: 0.8871 (m110) cc_final: 0.8668 (m110) REVERT: A 460 LYS cc_start: 0.7934 (tttm) cc_final: 0.7713 (tmtm) REVERT: A 478 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.7061 (p-80) REVERT: A 539 ASN cc_start: 0.8500 (t0) cc_final: 0.8188 (t0) REVERT: B 126 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7166 (mtp180) REVERT: B 180 MET cc_start: 0.8648 (mmm) cc_final: 0.8423 (tpt) REVERT: C 143 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7083 (pttp) REVERT: C 315 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.5888 (p90) outliers start: 22 outliers final: 14 residues processed: 115 average time/residue: 1.0037 time to fit residues: 125.0102 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 : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 57 ASP 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 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 28 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 0.0000 chunk 58 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 0.0000 chunk 66 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.139673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.114743 restraints weight = 8817.908| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.17 r_work: 0.3145 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 8871 Z= 0.136 Angle : 1.373 82.453 12113 Z= 0.403 Chirality : 0.060 1.463 1277 Planarity : 0.005 0.105 1572 Dihedral : 10.843 101.449 1306 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.14 % Allowed : 15.24 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1083 helix: 1.82 (0.27), residues: 393 sheet: 0.53 (0.66), residues: 71 loop : -0.42 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 PHE 0.014 0.001 PHE A 270 TYR 0.013 0.001 TYR A 443 ARG 0.002 0.000 ARG C 323 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 316) hydrogen bonds : angle 4.77481 ( 867) metal coordination : bond 0.00356 ( 3) metal coordination : angle 33.08272 ( 9) covalent geometry : bond 0.00297 ( 8857) covalent geometry : angle 1.03514 (12104) Misc. bond : bond 0.05707 ( 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 125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: A 456 MET cc_start: 0.8338 (mmt) cc_final: 0.8076 (mmm) REVERT: A 460 LYS cc_start: 0.7863 (tttm) cc_final: 0.7663 (tmtm) REVERT: A 478 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.6995 (p-80) REVERT: A 491 ASP cc_start: 0.7912 (t0) cc_final: 0.7383 (t0) REVERT: B 126 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7183 (mtp85) REVERT: B 180 MET cc_start: 0.8534 (mmm) cc_final: 0.8203 (mmp) REVERT: C 143 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7040 (pttp) REVERT: C 315 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.5869 (p90) outliers start: 19 outliers final: 14 residues processed: 116 average time/residue: 0.9905 time to fit residues: 124.4590 Evaluate side-chains 121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 57 ASP 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 0.2980 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.106593 restraints weight = 8883.943| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.20 r_work: 0.3041 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.279 8871 Z= 0.236 Angle : 1.464 81.416 12113 Z= 0.447 Chirality : 0.065 1.490 1277 Planarity : 0.006 0.113 1572 Dihedral : 11.643 111.023 1306 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.64 % Rotamer: Outliers : 2.48 % Allowed : 15.24 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 1083 helix: 1.49 (0.27), residues: 391 sheet: 0.42 (0.64), residues: 73 loop : -0.63 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 128 HIS 0.007 0.001 HIS C 200 PHE 0.020 0.002 PHE A 270 TYR 0.019 0.002 TYR A 79 ARG 0.002 0.000 ARG C 386 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 316) hydrogen bonds : angle 5.13079 ( 867) metal coordination : bond 0.00588 ( 3) metal coordination : angle 35.03511 ( 9) covalent geometry : bond 0.00556 ( 8857) covalent geometry : angle 1.10965 (12104) Misc. bond : bond 0.09467 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5669.13 seconds wall clock time: 98 minutes 34.77 seconds (5914.77 seconds total)