Starting phenix.real_space_refine on Thu Feb 13 19:07:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jek_36191/02_2025/8jek_36191.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jek_36191/02_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_36191/02_2025/8jek_36191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jek_36191/02_2025/8jek_36191.map" model { file = "/net/cci-nas-00/data/ceres_data/8jek_36191/02_2025/8jek_36191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jek_36191/02_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-5592/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: 5.48, per 1000 atoms: 0.64 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: 2.40 Conformation dependent library (CDL) restraints added in 1.0 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: 0.87 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: 2.19 Time building geometry restraints manager: 2.75 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: 1.560 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.950 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: 0.010 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.150 ------------------------------------------------------------------------------- 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 8857 Z= 1.597 Angle : 1.339 47.314 12104 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 *********************** 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 : 0.884 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: 1.1056 time to fit residues: 140.0605 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 : 1.030 ------------------------------------------------------------------------------- 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 8857 Z= 0.324 Angle : 1.323 68.807 12104 Z= 0.491 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 *********************** 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 : 0.945 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: 1.0598 time to fit residues: 138.7009 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 : 0.980 ------------------------------------------------------------------------------- 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: 6.9990 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: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.127199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.098090 restraints weight = 9323.990| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.57 r_work: 0.2955 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 8857 Z= 0.455 Angle : 1.157 86.215 12104 Z= 0.463 Chirality : 0.063 1.249 1277 Planarity : 0.006 0.107 1572 Dihedral : 12.377 150.440 1309 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 3.05 % Allowed : 13.32 % Favored : 83.63 % 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: -0.01 (0.25), residues: 1083 helix: 1.21 (0.26), residues: 385 sheet: 0.08 (0.63), residues: 76 loop : -0.81 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 173 HIS 0.007 0.001 HIS A 76 PHE 0.023 0.002 PHE A 80 TYR 0.022 0.002 TYR A 79 ARG 0.003 0.000 ARG C 323 *********************** 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 : 0.838 Fit side-chains revert: symmetry clash REVERT: A 478 HIS cc_start: 0.7826 (OUTLIER) cc_final: 0.7331 (p-80) REVERT: A 539 ASN cc_start: 0.8449 (t0) cc_final: 0.8102 (t0) REVERT: C 135 TYR cc_start: 0.8412 (t80) cc_final: 0.8197 (t80) REVERT: C 143 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7091 (pttp) outliers start: 27 outliers final: 16 residues processed: 121 average time/residue: 1.0653 time to fit residues: 138.9293 Evaluate side-chains 125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 384 MET 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: 0.9980 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.133502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107409 restraints weight = 8811.704| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.21 r_work: 0.3074 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 8857 Z= 0.242 Angle : 1.050 82.536 12104 Z= 0.410 Chirality : 0.061 1.456 1277 Planarity : 0.006 0.098 1572 Dihedral : 11.891 146.593 1308 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 2.71 % Allowed : 14.11 % 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 (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: 0.26 (0.26), residues: 1083 helix: 1.50 (0.27), residues: 387 sheet: 0.21 (0.63), residues: 73 loop : -0.70 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 111 HIS 0.004 0.001 HIS A 110 PHE 0.016 0.001 PHE A 270 TYR 0.017 0.001 TYR A 79 ARG 0.002 0.000 ARG C 323 *********************** 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 131 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8882 (m110) cc_final: 0.8630 (m110) REVERT: A 478 HIS cc_start: 0.7671 (OUTLIER) cc_final: 0.7262 (p-80) REVERT: A 539 ASN cc_start: 0.8527 (t0) cc_final: 0.8199 (t0) REVERT: C 143 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7132 (pttp) REVERT: C 315 TYR cc_start: 0.6893 (OUTLIER) cc_final: 0.6047 (p90) outliers start: 24 outliers final: 14 residues processed: 120 average time/residue: 1.0779 time to fit residues: 139.3766 Evaluate side-chains 121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 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: 0.0030 chunk 28 optimal weight: 0.0070 chunk 7 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.4408 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.136608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.111542 restraints weight = 8802.123| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.19 r_work: 0.3117 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 8857 Z= 0.206 Angle : 1.028 82.615 12104 Z= 0.396 Chirality : 0.060 1.450 1277 Planarity : 0.005 0.097 1572 Dihedral : 11.481 137.795 1308 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.71 % Allowed : 14.11 % 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 (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: 1.64 (0.27), residues: 393 sheet: 0.38 (0.64), residues: 71 loop : -0.56 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 323 *********************** 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 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8852 (m110) cc_final: 0.8646 (m110) REVERT: A 478 HIS cc_start: 0.7476 (OUTLIER) cc_final: 0.7073 (p-80) REVERT: A 539 ASN cc_start: 0.8485 (t0) cc_final: 0.8176 (t0) REVERT: B 126 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7165 (mtp85) REVERT: C 143 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7119 (pttp) REVERT: C 315 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.5745 (p90) outliers start: 24 outliers final: 12 residues processed: 116 average time/residue: 1.1189 time to fit residues: 140.0661 Evaluate side-chains 118 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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: 0.2980 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 59 optimal weight: 0.0980 chunk 97 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.138919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.113871 restraints weight = 8667.550| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.17 r_work: 0.3116 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 8857 Z= 0.206 Angle : 1.027 82.592 12104 Z= 0.394 Chirality : 0.060 1.457 1277 Planarity : 0.005 0.088 1572 Dihedral : 11.236 127.278 1308 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.93 % Allowed : 14.00 % 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: 0.60 (0.26), residues: 1083 helix: 1.73 (0.27), residues: 393 sheet: 0.42 (0.65), residues: 71 loop : -0.48 (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 110 PHE 0.014 0.001 PHE A 270 TYR 0.017 0.001 TYR A 79 ARG 0.002 0.000 ARG C 323 *********************** 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 134 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: A 478 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.7083 (p-80) REVERT: A 539 ASN cc_start: 0.8504 (t0) cc_final: 0.8199 (t0) REVERT: B 126 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7134 (mtp85) REVERT: C 143 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7112 (pttp) outliers start: 26 outliers final: 13 residues processed: 122 average time/residue: 1.0161 time to fit residues: 134.4776 Evaluate side-chains 118 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.135539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.109847 restraints weight = 8790.616| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.18 r_work: 0.3083 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 8857 Z= 0.270 Angle : 1.063 82.294 12104 Z= 0.414 Chirality : 0.062 1.464 1277 Planarity : 0.005 0.087 1572 Dihedral : 11.309 123.045 1306 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.89 % Favored : 95.01 % Rotamer: Outliers : 2.82 % Allowed : 14.33 % Favored : 82.84 % 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: 1.63 (0.27), residues: 393 sheet: 0.52 (0.65), residues: 71 loop : -0.54 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 128 HIS 0.005 0.001 HIS C 200 PHE 0.018 0.001 PHE A 270 TYR 0.022 0.001 TYR A 79 ARG 0.002 0.000 ARG C 323 *********************** 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 : 1.043 Fit side-chains revert: symmetry clash REVERT: A 460 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7714 (tmtm) REVERT: A 478 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.7214 (p-80) REVERT: A 539 ASN cc_start: 0.8531 (t0) cc_final: 0.8212 (t0) REVERT: B 126 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7222 (mtp180) REVERT: B 183 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.5693 (p90) REVERT: C 143 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7119 (pttp) outliers start: 25 outliers final: 15 residues processed: 114 average time/residue: 1.0949 time to fit residues: 134.8106 Evaluate side-chains 121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 460 LYS 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 267 MET Chi-restraints excluded: chain C residue 315 TYR 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: 0.9990 chunk 85 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 0.0870 chunk 102 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.136367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.111087 restraints weight = 8873.726| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.19 r_work: 0.3089 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 8857 Z= 0.234 Angle : 1.047 82.241 12104 Z= 0.404 Chirality : 0.062 1.469 1277 Planarity : 0.005 0.107 1572 Dihedral : 11.174 118.249 1306 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % 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: 0.55 (0.26), residues: 1083 helix: 1.67 (0.27), residues: 393 sheet: 0.50 (0.65), residues: 71 loop : -0.51 (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 C 200 PHE 0.016 0.001 PHE A 270 TYR 0.016 0.001 TYR A 79 ARG 0.002 0.000 ARG C 323 *********************** 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 123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: A 460 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7700 (tmtm) REVERT: A 478 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.7123 (p-80) REVERT: A 539 ASN cc_start: 0.8519 (t0) cc_final: 0.8198 (t0) REVERT: B 126 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7140 (mtp180) REVERT: C 143 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7127 (pttp) outliers start: 24 outliers final: 14 residues processed: 113 average time/residue: 1.0904 time to fit residues: 132.7648 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 : 0.927 ------------------------------------------------------------------------------- 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 460 LYS 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 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: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.133860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.107950 restraints weight = 8840.506| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.18 r_work: 0.3049 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 8857 Z= 0.316 Angle : 1.083 81.652 12104 Z= 0.425 Chirality : 0.064 1.489 1277 Planarity : 0.006 0.109 1572 Dihedral : 11.426 118.446 1306 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % 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 (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: 392 sheet: 0.40 (0.65), residues: 73 loop : -0.59 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 128 HIS 0.006 0.001 HIS C 200 PHE 0.019 0.002 PHE A 270 TYR 0.021 0.002 TYR A 79 ARG 0.002 0.000 ARG A 52 *********************** 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 126 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 478 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.7267 (p-80) REVERT: A 539 ASN cc_start: 0.8538 (t0) cc_final: 0.8210 (t0) REVERT: B 126 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7304 (mtp180) REVERT: C 143 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7089 (pttp) REVERT: C 315 TYR cc_start: 0.6890 (OUTLIER) cc_final: 0.5272 (p90) outliers start: 23 outliers final: 16 residues processed: 114 average time/residue: 1.1338 time to fit residues: 140.0216 Evaluate side-chains 122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 B residue 180 MET 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 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 28 optimal weight: 0.0570 chunk 30 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 0.0870 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.137740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.112397 restraints weight = 8836.560| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.18 r_work: 0.3106 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 8857 Z= 0.214 Angle : 1.044 82.277 12104 Z= 0.401 Chirality : 0.061 1.462 1277 Planarity : 0.005 0.111 1572 Dihedral : 11.038 110.677 1306 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.92 % Allowed : 15.58 % Favored : 82.51 % 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: 0.59 (0.26), residues: 1083 helix: 1.70 (0.27), residues: 393 sheet: 0.46 (0.65), residues: 71 loop : -0.47 (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 0.016 0.001 PHE A 270 TYR 0.014 0.001 TYR A 443 ARG 0.002 0.000 ARG C 323 ********************** 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 115 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: A 456 MET cc_start: 0.8339 (mmt) cc_final: 0.8069 (mmm) REVERT: A 478 HIS cc_start: 0.7503 (OUTLIER) cc_final: 0.7103 (p-80) REVERT: A 539 ASN cc_start: 0.8514 (t0) cc_final: 0.8205 (t0) REVERT: B 126 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7157 (mtp180) REVERT: C 143 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7074 (pttp) REVERT: C 315 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.5270 (p90) outliers start: 17 outliers final: 10 residues processed: 106 average time/residue: 1.0960 time to fit residues: 125.5510 Evaluate side-chains 113 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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 315 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 306 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.127908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.099096 restraints weight = 9411.182| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.57 r_work: 0.2963 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 8857 Z= 0.390 Angle : 1.112 81.435 12104 Z= 0.442 Chirality : 0.065 1.493 1277 Planarity : 0.006 0.119 1572 Dihedral : 11.723 116.714 1304 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.17 % Favored : 94.74 % Rotamer: Outliers : 2.14 % Allowed : 15.01 % Favored : 82.84 % 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: 0.28 (0.25), residues: 1083 helix: 1.41 (0.27), residues: 391 sheet: 0.39 (0.64), residues: 73 loop : -0.65 (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 0.021 0.002 PHE A 80 TYR 0.020 0.002 TYR A 79 ARG 0.002 0.000 ARG C 386 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6014.22 seconds wall clock time: 107 minutes 18.95 seconds (6438.95 seconds total)