Starting phenix.real_space_refine on Sat Jul 4 12:20:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pt6_17868/07_2026/8pt6_17868_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pt6_17868/07_2026/8pt6_17868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pt6_17868/07_2026/8pt6_17868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pt6_17868/07_2026/8pt6_17868.map" model { file = "/net/cci-nas-00/data/ceres_data/8pt6_17868/07_2026/8pt6_17868_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pt6_17868/07_2026/8pt6_17868_trim.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 8 Type Number sf(0) Gaussians Zn 3 6.06 5 P 31 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 6433 2.51 5 N 1828 2.21 5 O 2025 1.98 5 H 10051 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20436 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6652 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7971 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 515, 7970 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} Conformer: "B" Number of residues, atoms: 515, 7970 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} bond proxies already assigned to first conformer: 8041 Chain: "C" Number of atoms: 4887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 4887 Classifications: {'peptide': 310} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 292} Chain breaks: 1 Chain: "V" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 406 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "S" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 486 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 8} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CTP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2585 SG CYS A 161 44.562 50.821 17.982 1.00 61.93 S ATOM 4473 SG CYS A 282 42.322 48.732 15.482 1.00 64.89 S ATOM 16942 SG CYS C 146 29.762 69.730 80.614 1.00127.37 S ATOM 17130 SG CYS C 159 31.471 69.008 77.299 1.00111.13 S ATOM 17185 SG CYS C 163 32.787 71.906 79.371 1.00119.08 S ATOM 17195 SG CYS C 164 33.107 68.366 80.746 1.00108.45 S ATOM 18275 SG CYS C 233 36.504 91.333 70.828 1.00139.04 S ATOM 18300 SG CYS C 235 37.665 88.886 73.425 1.00130.85 S Time building chain proxies: 5.08, per 1000 atoms: 0.25 Number of scatterers: 20436 At special positions: 0 Unit cell: (89.04, 114.24, 124.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 S 63 16.00 P 31 15.00 Mg 2 11.99 O 2025 8.00 N 1828 7.00 C 6433 6.00 H 10051 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 770.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 159 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 146 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 164 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 191 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 184 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 235 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 233 " Number of angles added : 8 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 41.5% alpha, 13.9% beta 7 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.622A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.627A pdb=" N GLY A 168 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 235 removed outlier: 3.690A pdb=" N THR A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 312 through 323 removed outlier: 4.242A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.905A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.611A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.831A pdb=" N LEU B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 70' Processing helix chain 'B' and resid 92 through 104 Processing helix chain 'B' and resid 107 through 117 Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 161 through 183 Processing helix chain 'B' and resid 184 through 187 removed outlier: 3.619A pdb=" N THR B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 216 through 221 removed outlier: 3.571A pdb=" N ILE B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.750A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.849A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 356 through 372 Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.556A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 426 Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.925A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 removed outlier: 3.673A pdb=" N LYS B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 497 removed outlier: 3.650A pdb=" N LEU B 497 " --> pdb=" O HIS B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.553A pdb=" N HIS C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 42 through 55 Processing helix chain 'C' and resid 56 through 59 removed outlier: 3.509A pdb=" N LEU C 59 " --> pdb=" O LEU C 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 59' Processing helix chain 'C' and resid 87 through 98 Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 234 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.247A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.297A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.297A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA7, first strand: chain 'B' and resid 155 through 159 removed outlier: 3.666A pdb=" N ARG B 155 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AA9, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 83 removed outlier: 7.110A pdb=" N LYS C 75 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR C 119 " --> pdb=" O LYS C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 221 through 224 removed outlier: 3.856A pdb=" N CYS C 259 " --> pdb=" O GLY C 262 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL C 264 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ALA C 257 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 385 through 386 removed outlier: 3.795A pdb=" N ALA C 414 " --> pdb=" O CYS C 409 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 5.04 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10019 1.03 - 1.23: 44 1.23 - 1.42: 4497 1.42 - 1.62: 6061 1.62 - 1.81: 87 Bond restraints: 20708 Sorted by residual: bond pdb=" O3B CTP F 1 " pdb=" PG CTP F 1 " ideal model delta sigma weight residual 1.751 1.614 0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" O3A CTP F 1 " pdb=" PB CTP F 1 " ideal model delta sigma weight residual 1.675 1.601 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" O5' CTP F 1 " pdb=" PA CTP F 1 " ideal model delta sigma weight residual 1.660 1.604 0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" C5' CTP F 1 " pdb=" O5' CTP F 1 " ideal model delta sigma weight residual 1.405 1.451 -0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" C1' CTP F 1 " pdb=" N1 CTP F 1 " ideal model delta sigma weight residual 1.450 1.487 -0.037 2.00e-02 2.50e+03 3.50e+00 ... (remaining 20703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 36049 1.25 - 2.49: 1186 2.49 - 3.74: 141 3.74 - 4.99: 16 4.99 - 6.23: 5 Bond angle restraints: 37397 Sorted by residual: angle pdb=" N PHE C 258 " pdb=" CA PHE C 258 " pdb=" C PHE C 258 " ideal model delta sigma weight residual 114.56 110.72 3.84 1.27e+00 6.20e-01 9.13e+00 angle pdb=" N VAL B 203 " pdb=" CA VAL B 203 " pdb=" CB VAL B 203 " ideal model delta sigma weight residual 112.07 107.82 4.25 1.52e+00 4.33e-01 7.82e+00 angle pdb=" CA ARG B 475 " pdb=" CB ARG B 475 " pdb=" CG ARG B 475 " ideal model delta sigma weight residual 114.10 119.39 -5.29 2.00e+00 2.50e-01 7.00e+00 angle pdb=" CB ILE B 486 " pdb=" CG1 ILE B 486 " pdb=" CD1 ILE B 486 " ideal model delta sigma weight residual 113.80 118.81 -5.01 2.10e+00 2.27e-01 5.68e+00 angle pdb=" N ASP C 140 " pdb=" CA ASP C 140 " pdb=" C ASP C 140 " ideal model delta sigma weight residual 107.23 111.05 -3.82 1.67e+00 3.59e-01 5.24e+00 ... (remaining 37392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 9358 35.28 - 70.56: 420 70.56 - 105.84: 23 105.84 - 141.11: 0 141.11 - 176.39: 1 Dihedral angle restraints: 9802 sinusoidal: 5583 harmonic: 4219 Sorted by residual: dihedral pdb=" C4' G S 1 " pdb=" C3' G S 1 " pdb=" O3' G S 1 " pdb=" P U S 2 " ideal model delta sinusoidal sigma weight residual -110.00 66.39 -176.39 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA ARG B 394 " pdb=" C ARG B 394 " pdb=" N TYR B 395 " pdb=" CA TYR B 395 " ideal model delta harmonic sigma weight residual -180.00 -161.79 -18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA LEU B 265 " pdb=" C LEU B 265 " pdb=" N MET B 266 " pdb=" CA MET B 266 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 9799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1333 0.041 - 0.083: 211 0.083 - 0.124: 84 0.124 - 0.165: 6 0.165 - 0.207: 1 Chirality restraints: 1635 Sorted by residual: chirality pdb=" C2' CTP F 1 " pdb=" C1' CTP F 1 " pdb=" C3' CTP F 1 " pdb=" O2' CTP F 1 " both_signs ideal model delta sigma weight residual False -2.52 -2.73 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C3' G S 1 " pdb=" C4' G S 1 " pdb=" O3' G S 1 " pdb=" C2' G S 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.60 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" C1' CTP F 1 " pdb=" C2' CTP F 1 " pdb=" N1 CTP F 1 " pdb=" O4' CTP F 1 " both_signs ideal model delta sigma weight residual False 2.35 2.50 -0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 1632 not shown) Planarity restraints: 2961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 161 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO B 162 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A S 8 " 0.019 2.00e-02 2.50e+03 8.45e-03 2.32e+00 pdb=" N9 A S 8 " -0.023 2.00e-02 2.50e+03 pdb=" C8 A S 8 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A S 8 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A S 8 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A S 8 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A S 8 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A S 8 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A S 8 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A S 8 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A S 8 " 0.000 2.00e-02 2.50e+03 pdb=" H8 A S 8 " -0.000 2.00e-02 2.50e+03 pdb=" H2 A S 8 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 469 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO B 470 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " 0.019 5.00e-02 4.00e+02 ... (remaining 2958 not shown) Histogram of nonbonded interaction distances: 1.00 - 1.72: 25 1.72 - 2.44: 11247 2.44 - 3.16: 62150 3.16 - 3.88: 84118 3.88 - 4.60: 133872 Warning: very small nonbonded interaction distances. Nonbonded interactions: 291412 Sorted by model distance: nonbonded pdb=" HD2 HIS C 266 " pdb="HG13 VAL C 269 " model vdw 0.997 2.270 nonbonded pdb=" HB2 CYS C 233 " pdb="ZN ZN C 502 " model vdw 1.374 1.544 nonbonded pdb=" OE1 GLU C 89 " pdb=" H GLU C 89 " model vdw 1.484 2.450 nonbonded pdb=" O GLY A 309 " pdb="HH22 ARG B 394 " model vdw 1.559 2.450 nonbonded pdb=" OD2 ASP A 43 " pdb=" H PHE A 55 " model vdw 1.574 2.450 ... (remaining 291407 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=0.40 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: 2.370 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: 0.110 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 30.430 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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 : 0.003 0.137 10669 Z= 0.141 Angle : 0.514 7.812 14545 Z= 0.269 Chirality : 0.037 0.207 1635 Planarity : 0.003 0.051 1765 Dihedral : 18.519 176.392 4187 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 2.43 % Allowed : 25.02 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.25), residues: 1234 helix: 1.99 (0.25), residues: 477 sheet: 0.43 (0.42), residues: 150 loop : -0.22 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 475 TYR 0.009 0.001 TYR A 403 PHE 0.010 0.001 PHE C 44 TRP 0.005 0.001 TRP C 183 HIS 0.002 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (10657) covalent geometry : angle 0.50373 / 0.27 (14537) hydrogen bonds : bond 0.11653 / 7.31 ( 441) hydrogen bonds : angle 5.41971 / 3.74 ( 1219) metal coordination : bond 0.01863 / 1.46 ( 12) metal coordination : angle 4.46542 / 2.48 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7725 (pm20) REVERT: B 219 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7781 (mp0) outliers start: 26 outliers final: 23 residues processed: 115 average time/residue: 0.2600 time to fit residues: 41.1042 Evaluate side-chains 112 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.149439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.104219 restraints weight = 41858.197| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.25 r_work: 0.3074 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10669 Z= 0.149 Angle : 0.511 8.102 14545 Z= 0.266 Chirality : 0.038 0.141 1635 Planarity : 0.004 0.053 1765 Dihedral : 13.523 168.439 1853 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.89 % Favored : 96.03 % Rotamer: Outliers : 2.33 % Allowed : 23.72 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.24), residues: 1234 helix: 1.88 (0.24), residues: 477 sheet: 0.51 (0.43), residues: 144 loop : -0.28 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 394 TYR 0.012 0.001 TYR A 403 PHE 0.013 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (10657) covalent geometry : angle 0.50524 / 0.27 (14537) hydrogen bonds : bond 0.04743 / 3.12 ( 441) hydrogen bonds : angle 4.72366 / 3.25 ( 1219) metal coordination : bond 0.01932 / 1.48 ( 12) metal coordination : angle 3.32752 / 1.89 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8500 (mp) outliers start: 25 outliers final: 15 residues processed: 108 average time/residue: 0.2855 time to fit residues: 42.2461 Evaluate side-chains 101 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 56 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.148433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.102072 restraints weight = 41696.292| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.17 r_work: 0.3056 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10669 Z= 0.170 Angle : 0.506 8.324 14545 Z= 0.262 Chirality : 0.038 0.137 1635 Planarity : 0.004 0.052 1765 Dihedral : 12.779 167.259 1833 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.13 % Favored : 95.79 % Rotamer: Outliers : 2.52 % Allowed : 22.88 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.24), residues: 1234 helix: 1.81 (0.24), residues: 478 sheet: 0.50 (0.42), residues: 142 loop : -0.37 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 73 TYR 0.014 0.001 TYR A 403 PHE 0.014 0.001 PHE C 44 TRP 0.007 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (10657) covalent geometry : angle 0.49984 / 0.26 (14537) hydrogen bonds : bond 0.04540 / 3.03 ( 441) hydrogen bonds : angle 4.58110 / 3.15 ( 1219) metal coordination : bond 0.02087 / 1.54 ( 12) metal coordination : angle 3.48770 / 1.95 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8555 (mp) REVERT: B 219 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.7961 (mt-10) REVERT: B 222 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8071 (t70) outliers start: 27 outliers final: 18 residues processed: 105 average time/residue: 0.2631 time to fit residues: 38.3894 Evaluate side-chains 106 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 62 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.149069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.103283 restraints weight = 41855.677| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.25 r_work: 0.3062 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10669 Z= 0.127 Angle : 0.484 8.843 14545 Z= 0.250 Chirality : 0.037 0.137 1635 Planarity : 0.004 0.052 1765 Dihedral : 12.454 166.501 1832 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 2.24 % Allowed : 23.16 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.24), residues: 1234 helix: 1.85 (0.24), residues: 478 sheet: 0.43 (0.43), residues: 144 loop : -0.34 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 73 TYR 0.012 0.001 TYR A 403 PHE 0.013 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10657) covalent geometry : angle 0.47735 / 0.25 (14537) hydrogen bonds : bond 0.04093 / 2.74 ( 441) hydrogen bonds : angle 4.44684 / 3.07 ( 1219) metal coordination : bond 0.02141 / 1.65 ( 12) metal coordination : angle 3.54907 / 2.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8405 (mppt) REVERT: B 121 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8556 (mp) REVERT: B 222 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8077 (t70) outliers start: 24 outliers final: 15 residues processed: 107 average time/residue: 0.3116 time to fit residues: 44.4571 Evaluate side-chains 104 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 123 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.147864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102679 restraints weight = 41582.519| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.47 r_work: 0.3033 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10669 Z= 0.161 Angle : 0.493 8.587 14545 Z= 0.256 Chirality : 0.037 0.134 1635 Planarity : 0.004 0.052 1765 Dihedral : 12.261 166.432 1830 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.33 % Allowed : 23.06 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.24), residues: 1234 helix: 1.80 (0.24), residues: 478 sheet: 0.43 (0.43), residues: 142 loop : -0.42 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 TYR 0.014 0.001 TYR A 403 PHE 0.014 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (10657) covalent geometry : angle 0.48635 / 0.26 (14537) hydrogen bonds : bond 0.04243 / 2.84 ( 441) hydrogen bonds : angle 4.41139 / 3.05 ( 1219) metal coordination : bond 0.02127 / 1.59 ( 12) metal coordination : angle 3.55640 / 2.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8385 (mppt) REVERT: B 121 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8553 (mp) REVERT: B 219 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: B 222 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8115 (t70) REVERT: C 185 MET cc_start: 0.4458 (mtm) cc_final: 0.4217 (mtm) outliers start: 25 outliers final: 18 residues processed: 105 average time/residue: 0.3056 time to fit residues: 43.0764 Evaluate side-chains 104 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.147186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102219 restraints weight = 41491.780| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.36 r_work: 0.3028 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10669 Z= 0.188 Angle : 0.507 8.586 14545 Z= 0.264 Chirality : 0.038 0.138 1635 Planarity : 0.004 0.053 1765 Dihedral : 12.221 166.505 1828 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.61 % Allowed : 22.13 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.24), residues: 1234 helix: 1.73 (0.24), residues: 478 sheet: 0.35 (0.42), residues: 142 loop : -0.44 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 TYR 0.014 0.001 TYR A 403 PHE 0.015 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (10657) covalent geometry : angle 0.49966 / 0.26 (14537) hydrogen bonds : bond 0.04376 / 2.93 ( 441) hydrogen bonds : angle 4.43280 / 3.07 ( 1219) metal coordination : bond 0.02179 / 1.58 ( 12) metal coordination : angle 3.67421 / 2.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8411 (mppt) REVERT: A 317 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7912 (ttm170) REVERT: B 121 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8587 (mp) REVERT: B 219 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: B 222 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8119 (t70) outliers start: 28 outliers final: 20 residues processed: 110 average time/residue: 0.2705 time to fit residues: 40.4043 Evaluate side-chains 108 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 107 optimal weight: 0.0570 chunk 33 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.0070 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.149167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.104474 restraints weight = 41189.995| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.25 r_work: 0.3067 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 10669 Z= 0.093 Angle : 0.469 9.151 14545 Z= 0.242 Chirality : 0.037 0.141 1635 Planarity : 0.004 0.051 1765 Dihedral : 12.159 166.259 1827 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.05 % Allowed : 22.41 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.24), residues: 1234 helix: 1.93 (0.24), residues: 478 sheet: 0.41 (0.43), residues: 144 loop : -0.31 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 TYR 0.009 0.001 TYR A 403 PHE 0.011 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (10657) covalent geometry : angle 0.46145 / 0.24 (14537) hydrogen bonds : bond 0.03730 / 2.50 ( 441) hydrogen bonds : angle 4.27779 / 2.95 ( 1219) metal coordination : bond 0.02195 / 1.72 ( 12) metal coordination : angle 3.61870 / 2.07 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8363 (mppt) REVERT: B 33 ARG cc_start: 0.8114 (mtp180) cc_final: 0.7778 (mtp180) REVERT: B 219 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: B 222 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8081 (t70) outliers start: 22 outliers final: 17 residues processed: 109 average time/residue: 0.2973 time to fit residues: 43.9599 Evaluate side-chains 106 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 104 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.147297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.100720 restraints weight = 41595.361| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.19 r_work: 0.3029 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10669 Z= 0.176 Angle : 0.500 8.758 14545 Z= 0.259 Chirality : 0.038 0.133 1635 Planarity : 0.004 0.052 1765 Dihedral : 12.168 166.318 1827 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.15 % Allowed : 22.60 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.24), residues: 1234 helix: 1.83 (0.24), residues: 478 sheet: 0.29 (0.42), residues: 142 loop : -0.38 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 217 TYR 0.014 0.001 TYR A 403 PHE 0.019 0.001 PHE C 253 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (10657) covalent geometry : angle 0.49235 / 0.26 (14537) hydrogen bonds : bond 0.04199 / 2.81 ( 441) hydrogen bonds : angle 4.32621 / 3.00 ( 1219) metal coordination : bond 0.02214 / 1.63 ( 12) metal coordination : angle 3.67939 / 2.07 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8442 (mppt) REVERT: B 222 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8135 (t70) REVERT: C 217 ARG cc_start: 0.5829 (OUTLIER) cc_final: 0.5359 (ttt-90) outliers start: 23 outliers final: 17 residues processed: 105 average time/residue: 0.3068 time to fit residues: 43.6096 Evaluate side-chains 105 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.147911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.103250 restraints weight = 41099.639| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.24 r_work: 0.3049 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10669 Z= 0.124 Angle : 0.478 9.110 14545 Z= 0.248 Chirality : 0.037 0.138 1635 Planarity : 0.004 0.052 1765 Dihedral : 12.168 166.355 1827 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.96 % Allowed : 22.60 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1234 helix: 1.85 (0.24), residues: 478 sheet: 0.29 (0.42), residues: 142 loop : -0.36 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 217 TYR 0.012 0.001 TYR A 403 PHE 0.013 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (10657) covalent geometry : angle 0.46996 / 0.25 (14537) hydrogen bonds : bond 0.03952 / 2.65 ( 441) hydrogen bonds : angle 4.28099 / 2.96 ( 1219) metal coordination : bond 0.02195 / 1.69 ( 12) metal coordination : angle 3.71898 / 2.11 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8434 (mppt) REVERT: B 216 LYS cc_start: 0.8455 (mttt) cc_final: 0.8204 (mmtt) REVERT: B 222 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8086 (t70) REVERT: C 185 MET cc_start: 0.4349 (mtm) cc_final: 0.4085 (mtm) outliers start: 21 outliers final: 18 residues processed: 106 average time/residue: 0.2940 time to fit residues: 42.6159 Evaluate side-chains 106 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.148171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.102706 restraints weight = 41287.338| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.37 r_work: 0.3041 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10669 Z= 0.129 Angle : 0.479 9.035 14545 Z= 0.248 Chirality : 0.037 0.137 1635 Planarity : 0.004 0.052 1765 Dihedral : 12.133 166.313 1826 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.87 % Allowed : 22.60 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1234 helix: 1.87 (0.24), residues: 478 sheet: 0.10 (0.42), residues: 147 loop : -0.34 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 217 TYR 0.013 0.001 TYR A 403 PHE 0.013 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (10657) covalent geometry : angle 0.47070 / 0.25 (14537) hydrogen bonds : bond 0.03904 / 2.61 ( 441) hydrogen bonds : angle 4.23357 / 2.94 ( 1219) metal coordination : bond 0.02153 / 1.65 ( 12) metal coordination : angle 3.71724 / 2.10 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8440 (mppt) REVERT: B 216 LYS cc_start: 0.8446 (mttt) cc_final: 0.8204 (mmtt) REVERT: B 222 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8113 (t70) outliers start: 20 outliers final: 17 residues processed: 103 average time/residue: 0.2865 time to fit residues: 39.9784 Evaluate side-chains 103 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 17 optimal weight: 0.0470 chunk 90 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 0.0070 chunk 94 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.104371 restraints weight = 41334.595| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.37 r_work: 0.3065 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 10669 Z= 0.093 Angle : 0.463 9.231 14545 Z= 0.239 Chirality : 0.036 0.139 1635 Planarity : 0.004 0.051 1765 Dihedral : 12.042 166.266 1825 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.59 % Allowed : 22.88 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.25), residues: 1234 helix: 1.98 (0.24), residues: 478 sheet: 0.12 (0.42), residues: 149 loop : -0.27 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 217 TYR 0.010 0.001 TYR A 403 PHE 0.011 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 (10657) covalent geometry : angle 0.45509 / 0.24 (14537) hydrogen bonds : bond 0.03573 / 2.39 ( 441) hydrogen bonds : angle 4.15669 / 2.88 ( 1219) metal coordination : bond 0.02217 / 1.74 ( 12) metal coordination : angle 3.73371 / 2.11 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6618.02 seconds wall clock time: 112 minutes 57.34 seconds (6777.34 seconds total)