Starting phenix.real_space_refine on Fri Aug 7 09:26:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pt6_17868/08_2026/8pt6_17868_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pt6_17868/08_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_17868/08_2026/8pt6_17868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pt6_17868/08_2026/8pt6_17868.map" model { file = "/net/cci-nas-00/data/ceres_data/8pt6_17868/08_2026/8pt6_17868_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pt6_17868/08_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-2.2rc3-6140/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: 3.85, per 1000 atoms: 0.19 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: 1.58 Conformation dependent library (CDL) restraints added in 560.3 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: 3.05 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: 4.27 Time building geometry restraints manager: 2.16 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: 35967 1.25 - 2.49: 1265 2.49 - 3.74: 144 3.74 - 4.99: 16 4.99 - 6.23: 5 Bond angle restraints: 37397 Sorted by residual: angle pdb=" O5' U S 13 " pdb=" C5' U S 13 " pdb=" C4' U S 13 " ideal model delta sigma weight residual 109.40 112.16 -2.76 8.00e-01 1.56e+00 1.19e+01 angle pdb=" O5' G S 3 " pdb=" C5' G S 3 " pdb=" C4' G S 3 " ideal model delta sigma weight residual 109.40 112.08 -2.68 8.00e-01 1.56e+00 1.13e+01 angle pdb=" O5' A S 7 " pdb=" C5' A S 7 " pdb=" C4' A S 7 " ideal model delta sigma weight residual 109.40 111.95 -2.55 8.00e-01 1.56e+00 1.01e+01 angle pdb=" O5' U V 12 " pdb=" C5' U V 12 " pdb=" C4' U V 12 " ideal model delta sigma weight residual 109.40 111.83 -2.43 8.00e-01 1.56e+00 9.19e+00 angle pdb=" O5' C V 13 " pdb=" C5' C V 13 " pdb=" C4' C V 13 " ideal model delta sigma weight residual 109.40 111.82 -2.42 8.00e-01 1.56e+00 9.13e+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: 1305 0.041 - 0.083: 212 0.083 - 0.124: 111 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: 1.690 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: 0.080 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 25.240 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.540 ------------------------------------------------------------------------------- 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= 0.143 Angle : 0.534 7.812 14545 Z= 0.300 Chirality : 0.039 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 0.00293 / 0.14 (10657) covalent geometry : angle 0.52423 / 0.30 (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 : 0.524 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: 0.2466 time to fit residues: 39.4865 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 : 0.350 ------------------------------------------------------------------------------- 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: 6.9990 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 = 0.3824 r_free = 0.3824 target = 0.149569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.104189 restraints weight = 41922.718| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.22 r_work: 0.3070 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- 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 = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0430 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= 0.148 Angle : 0.516 8.102 14545 Z= 0.267 Chirality : 0.038 0.239 1635 Planarity : 0.004 0.053 1765 Dihedral : 13.492 168.070 1853 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 2.43 % Allowed : 23.44 % Favored : 74.14 % 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: 0.96 (0.24), residues: 1234 helix: 1.86 (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 0.00330 / 0.15 (10657) covalent geometry : angle 0.50989 / 0.27 (14537) hydrogen bonds : bond 0.04669 / 3.07 ( 441) hydrogen bonds : angle 4.71936 / 3.24 ( 1219) metal coordination : bond 0.01946 / 1.49 ( 12) metal coordination : angle 3.33108 / 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 112 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8499 (mp) outliers start: 26 outliers final: 16 residues processed: 109 average time/residue: 0.2384 time to fit residues: 35.4437 Evaluate side-chains 102 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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=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: 0.9980 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.149449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.104135 restraints weight = 41635.247| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.21 r_work: 0.3071 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10669 Z= 0.135 Angle : 0.492 8.444 14545 Z= 0.253 Chirality : 0.038 0.231 1635 Planarity : 0.004 0.052 1765 Dihedral : 12.748 167.984 1833 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 2.33 % Allowed : 23.25 % Favored : 74.42 % 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: 0.96 (0.24), residues: 1234 helix: 1.89 (0.24), residues: 478 sheet: 0.57 (0.43), residues: 142 loop : -0.32 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 TYR 0.012 0.001 TYR A 403 PHE 0.013 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 0.00304 / 0.13 (10657) covalent geometry : angle 0.48586 / 0.25 (14537) hydrogen bonds : bond 0.04349 / 2.89 ( 441) hydrogen bonds : angle 4.56079 / 3.14 ( 1219) metal coordination : bond 0.02014 / 1.54 ( 12) metal coordination : angle 3.38457 / 1.92 ( 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 110 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8533 (mp) REVERT: B 222 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8078 (t70) outliers start: 25 outliers final: 18 residues processed: 104 average time/residue: 0.2603 time to fit residues: 37.7963 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 : 0.613 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.148171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.102330 restraints weight = 41940.776| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.26 r_work: 0.3049 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.0820 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= 0.173 Angle : 0.508 8.730 14545 Z= 0.262 Chirality : 0.038 0.230 1635 Planarity : 0.004 0.053 1765 Dihedral : 12.467 167.286 1832 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.52 % Allowed : 22.78 % Favored : 74.70 % 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: 1.79 (0.24), residues: 478 sheet: 0.43 (0.43), residues: 142 loop : -0.38 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 73 TYR 0.015 0.001 TYR A 403 PHE 0.015 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 0.00394 / 0.17 (10657) covalent geometry : angle 0.50102 / 0.26 (14537) hydrogen bonds : bond 0.04357 / 2.91 ( 441) hydrogen bonds : angle 4.48402 / 3.10 ( 1219) metal coordination : bond 0.02205 / 1.63 ( 12) metal coordination : angle 3.68824 / 2.08 ( 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 116 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8417 (mppt) REVERT: B 121 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8560 (mp) REVERT: B 219 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: B 222 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8087 (t70) outliers start: 27 outliers final: 18 residues processed: 111 average time/residue: 0.2980 time to fit residues: 44.5933 Evaluate side-chains 108 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 123 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 97 optimal weight: 0.0970 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.148598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.103260 restraints weight = 41547.024| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.30 r_work: 0.3051 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10669 Z= 0.126 Angle : 0.483 8.785 14545 Z= 0.248 Chirality : 0.038 0.230 1635 Planarity : 0.004 0.052 1765 Dihedral : 12.247 167.211 1830 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.33 % Allowed : 23.25 % Favored : 74.42 % 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: 1.85 (0.24), residues: 478 sheet: 0.32 (0.42), residues: 144 loop : -0.35 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 0.00283 / 0.12 (10657) covalent geometry : angle 0.47579 / 0.25 (14537) hydrogen bonds : bond 0.04081 / 2.73 ( 441) hydrogen bonds : angle 4.39841 / 3.03 ( 1219) metal coordination : bond 0.02179 / 1.67 ( 12) metal coordination : angle 3.53746 / 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 109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8367 (mppt) REVERT: B 121 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8523 (mp) REVERT: B 219 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: B 222 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8070 (t70) outliers start: 25 outliers final: 17 residues processed: 106 average time/residue: 0.3038 time to fit residues: 43.5406 Evaluate side-chains 104 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.147249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102067 restraints weight = 41539.150| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.29 r_work: 0.3028 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- 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 = 0.26 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 = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1065 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= 0.183 Angle : 0.510 8.699 14545 Z= 0.263 Chirality : 0.038 0.226 1635 Planarity : 0.004 0.053 1765 Dihedral : 12.173 167.440 1828 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.15 % Allowed : 22.78 % Favored : 75.07 % 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: 1.72 (0.24), residues: 478 sheet: 0.28 (0.43), residues: 142 loop : -0.42 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 73 TYR 0.015 0.001 TYR A 403 PHE 0.016 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 0.00416 / 0.18 (10657) covalent geometry : angle 0.50201 / 0.26 (14537) hydrogen bonds : bond 0.04364 / 2.92 ( 441) hydrogen bonds : angle 4.41711 / 3.06 ( 1219) metal coordination : bond 0.02223 / 1.62 ( 12) metal coordination : angle 3.75161 / 2.09 ( 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 110 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8408 (mppt) REVERT: B 121 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8595 (mp) REVERT: B 219 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: B 222 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8131 (t70) outliers start: 23 outliers final: 18 residues processed: 107 average time/residue: 0.2591 time to fit residues: 37.4071 Evaluate side-chains 103 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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 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 115 GLU 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: 1.9990 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 107 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.148225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.103272 restraints weight = 41345.648| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.35 r_work: 0.3044 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 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 = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10669 Z= 0.125 Angle : 0.482 9.034 14545 Z= 0.248 Chirality : 0.038 0.229 1635 Planarity : 0.004 0.052 1765 Dihedral : 12.137 167.070 1827 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 2.43 % Allowed : 22.50 % Favored : 75.07 % 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: 1.84 (0.24), residues: 478 sheet: 0.31 (0.43), residues: 142 loop : -0.36 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 TYR 0.011 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 0.00287 / 0.12 (10657) covalent geometry : angle 0.47441 / 0.25 (14537) hydrogen bonds : bond 0.04010 / 2.68 ( 441) hydrogen bonds : angle 4.32962 / 2.99 ( 1219) metal coordination : bond 0.02170 / 1.66 ( 12) metal coordination : angle 3.66506 / 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 111 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8407 (mppt) REVERT: B 222 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8114 (t70) outliers start: 26 outliers final: 20 residues processed: 108 average time/residue: 0.2522 time to fit residues: 37.3580 Evaluate side-chains 108 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 104 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 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: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.146727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.101161 restraints weight = 41682.452| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.33 r_work: 0.3016 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10669 Z= 0.197 Angle : 0.519 8.679 14545 Z= 0.269 Chirality : 0.039 0.224 1635 Planarity : 0.004 0.053 1765 Dihedral : 12.192 167.609 1827 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.43 % Allowed : 22.41 % Favored : 75.16 % 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: 0.66 (0.24), residues: 1234 helix: 1.68 (0.24), residues: 478 sheet: 0.18 (0.42), residues: 142 loop : -0.46 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 TYR 0.016 0.001 TYR A 403 PHE 0.016 0.001 PHE C 44 TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (10657) covalent geometry : angle 0.51158 / 0.27 (14537) hydrogen bonds : bond 0.04466 / 2.99 ( 441) hydrogen bonds : angle 4.40466 / 3.05 ( 1219) metal coordination : bond 0.02262 / 1.62 ( 12) metal coordination : angle 3.84549 / 2.12 ( 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 113 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8443 (mppt) REVERT: A 317 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7924 (ttm170) REVERT: B 121 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8627 (mp) REVERT: B 216 LYS cc_start: 0.8542 (mttt) cc_final: 0.8280 (mmtt) REVERT: B 222 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8146 (t70) REVERT: B 264 MET cc_start: 0.8913 (ptt) cc_final: 0.8706 (ptt) outliers start: 26 outliers final: 20 residues processed: 110 average time/residue: 0.2718 time to fit residues: 40.5976 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 : 0.540 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 114 optimal weight: 0.9990 chunk 94 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 124 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.148111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.103084 restraints weight = 41124.652| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.44 r_work: 0.3038 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- 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 = 0.28 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 = 0.29 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: 0.8518 moved from start: 0.1250 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= 0.119 Angle : 0.482 9.096 14545 Z= 0.248 Chirality : 0.038 0.230 1635 Planarity : 0.004 0.052 1765 Dihedral : 12.158 167.140 1827 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.15 % Allowed : 22.41 % 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: 0.78 (0.24), residues: 1234 helix: 1.79 (0.24), residues: 478 sheet: 0.20 (0.43), residues: 142 loop : -0.39 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 TYR 0.012 0.001 TYR A 403 PHE 0.013 0.001 PHE C 44 TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10657) covalent geometry : angle 0.47333 / 0.25 (14537) hydrogen bonds : bond 0.03998 / 2.67 ( 441) hydrogen bonds : angle 4.31325 / 2.98 ( 1219) metal coordination : bond 0.02192 / 1.68 ( 12) metal coordination : angle 3.80211 / 2.13 ( 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 111 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8433 (mppt) REVERT: B 216 LYS cc_start: 0.8477 (mttt) cc_final: 0.8236 (mmtt) REVERT: B 222 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8095 (t70) REVERT: C 185 MET cc_start: 0.4406 (mtm) cc_final: 0.4106 (mtm) outliers start: 23 outliers final: 19 residues processed: 108 average time/residue: 0.2712 time to fit residues: 39.9979 Evaluate side-chains 109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 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 248 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.147874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.102613 restraints weight = 41287.691| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.46 r_work: 0.3030 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.085 | | 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) = 0.085 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1270 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= 0.136 Angle : 0.493 8.887 14545 Z= 0.255 Chirality : 0.038 0.228 1635 Planarity : 0.004 0.052 1765 Dihedral : 12.144 167.230 1827 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.96 % Allowed : 22.69 % Favored : 75.35 % 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: 0.78 (0.24), residues: 1234 helix: 1.79 (0.24), residues: 478 sheet: 0.20 (0.43), residues: 142 loop : -0.39 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 TYR 0.013 0.001 TYR A 403 PHE 0.013 0.001 PHE C 44 TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (10657) covalent geometry : angle 0.48522 / 0.25 (14537) hydrogen bonds : bond 0.04019 / 2.69 ( 441) hydrogen bonds : angle 4.30379 / 2.98 ( 1219) metal coordination : bond 0.02169 / 1.65 ( 12) metal coordination : angle 3.74402 / 2.09 ( 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 108 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8446 (mppt) REVERT: B 216 LYS cc_start: 0.8479 (mttt) cc_final: 0.8236 (mmtt) REVERT: B 222 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8108 (t70) REVERT: C 185 MET cc_start: 0.4450 (mtm) cc_final: 0.4145 (mtm) outliers start: 21 outliers final: 18 residues processed: 105 average time/residue: 0.2559 time to fit residues: 36.7063 Evaluate side-chains 107 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 17 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 108 optimal weight: 0.0470 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.149018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.103513 restraints weight = 41280.563| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.29 r_work: 0.3060 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 10669 Z= 0.098 Angle : 0.478 9.309 14545 Z= 0.246 Chirality : 0.037 0.231 1635 Planarity : 0.004 0.052 1765 Dihedral : 12.034 166.913 1825 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.68 % Allowed : 22.97 % Favored : 75.35 % 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: 0.93 (0.24), residues: 1234 helix: 1.94 (0.24), residues: 478 sheet: 0.28 (0.43), residues: 142 loop : -0.34 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 245 TYR 0.011 0.001 TYR A 403 PHE 0.012 0.001 PHE C 243 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 0.00222 / 0.10 (10657) covalent geometry : angle 0.46960 / 0.24 (14537) hydrogen bonds : bond 0.03660 / 2.45 ( 441) hydrogen bonds : angle 4.20745 / 2.91 ( 1219) metal coordination : bond 0.02178 / 1.71 ( 12) metal coordination : angle 3.72742 / 2.11 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5897.79 seconds wall clock time: 100 minutes 34.06 seconds (6034.06 seconds total)