Starting phenix.real_space_refine on Sun Aug 24 21:13:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qz8_18772/08_2025/8qz8_18772.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qz8_18772/08_2025/8qz8_18772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qz8_18772/08_2025/8qz8_18772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qz8_18772/08_2025/8qz8_18772.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qz8_18772/08_2025/8qz8_18772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qz8_18772/08_2025/8qz8_18772.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.072 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 45 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 7113 2.51 5 N 2035 2.21 5 O 2292 1.98 5 H 11077 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22629 Number of models: 1 Model: "" Number of chains: 8 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: 7910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 7910 Classifications: {'peptide': 512} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 491} Chain breaks: 1 Chain: "C" Number of atoms: 6696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 6696 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain: "V" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1046 Classifications: {'RNA': 33} Modifications used: {'3*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 8, 'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna2p': 17, 'rna3p': 15} Chain breaks: 1 Chain: "P" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 289 Classifications: {'RNA': 9} Modifications used: {'3*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2585 SG CYS A 161 47.930 47.016 19.706 1.00 76.37 S ATOM 4473 SG CYS A 282 45.639 45.224 17.052 1.00 87.29 S ATOM 18195 SG CYS C 233 21.177 52.353 108.814 1.00129.37 S ATOM 18219 SG CYS C 235 21.445 54.226 105.382 1.00120.87 S ATOM 16861 SG CYS C 146 9.859 61.301 88.729 1.00133.35 S ATOM 17049 SG CYS C 159 9.623 64.497 90.979 1.00131.26 S ATOM 17105 SG CYS C 163 12.623 62.252 91.247 1.00119.92 S ATOM 17115 SG CYS C 164 12.238 64.813 88.738 1.00123.42 S Time building chain proxies: 4.34, per 1000 atoms: 0.19 Number of scatterers: 22629 At special positions: 0 Unit cell: (92.19, 101.848, 125.554, 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 45 15.00 Mg 1 11.99 O 2292 8.00 N 2035 7.00 C 7113 6.00 H 11077 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: 2.13 Conformation dependent library (CDL) restraints added in 691.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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 161 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 191 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 184 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 235 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 233 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 159 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 164 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 146 " Number of angles added : 8 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2546 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 15 sheets defined 41.7% alpha, 14.0% beta 10 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 4.83 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 13 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: 3.538A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 301 through 311 removed outlier: 3.665A pdb=" N GLN A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.936A pdb=" N THR A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 4.297A 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: 3.901A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.733A 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: 3.567A pdb=" N TYR B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 107 through 117 Processing helix chain 'B' and resid 129 through 138 removed outlier: 3.660A pdb=" N ARG B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 183 removed outlier: 4.020A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 236 through 248 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.687A 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 removed outlier: 3.607A pdb=" N SER B 372 " --> pdb=" O GLY B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.894A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 480 through 497 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 3 through 8 removed outlier: 3.534A pdb=" N PHE C 8 " --> pdb=" O PHE C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 23 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 42 through 54 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 108 Processing helix chain 'C' and resid 144 through 152 removed outlier: 3.655A pdb=" N SER C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 281 through 289 Processing helix chain 'C' and resid 303 through 317 removed outlier: 4.415A pdb=" N ARG C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 421 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.663A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.632A pdb=" N PHE B 291 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.614A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 202 " --> pdb=" O MET A 255 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.614A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 202 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 160 removed outlier: 7.072A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AB1, first strand: chain 'B' and resid 477 through 479 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 81 Processing sheet with id=AB4, first strand: chain 'C' and resid 221 through 224 removed outlier: 6.943A pdb=" N GLY C 262 " --> pdb=" O PHE C 258 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 360 through 363 Processing sheet with id=AB6, first strand: chain 'C' and resid 383 through 388 removed outlier: 3.614A pdb=" N THR C 385 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET C 415 " --> pdb=" O LEU C 387 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 5.41 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11045 1.04 - 1.24: 1512 1.24 - 1.44: 3735 1.44 - 1.65: 6568 1.65 - 1.85: 90 Bond restraints: 22950 Sorted by residual: bond pdb=" CB CYS C 146 " pdb=" SG CYS C 146 " ideal model delta sigma weight residual 1.808 1.776 0.032 3.30e-02 9.18e+02 9.37e-01 bond pdb=" C3' A V 29 " pdb=" O3' A V 29 " ideal model delta sigma weight residual 1.427 1.440 -0.013 1.50e-02 4.44e+03 7.70e-01 bond pdb=" CA ASN A 50 " pdb=" CB ASN A 50 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.51e-02 4.39e+03 7.57e-01 bond pdb=" N SER B 288 " pdb=" CA SER B 288 " ideal model delta sigma weight residual 1.471 1.456 0.015 1.74e-02 3.30e+03 7.30e-01 bond pdb=" CB CYS C 146 " pdb=" HB2 CYS C 146 " ideal model delta sigma weight residual 0.970 0.953 0.017 2.00e-02 2.50e+03 7.16e-01 ... (remaining 22945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 38440 0.96 - 1.91: 2699 1.91 - 2.87: 207 2.87 - 3.83: 82 3.83 - 4.79: 7 Bond angle restraints: 41435 Sorted by residual: angle pdb=" C SER B 288 " pdb=" CA SER B 288 " pdb=" CB SER B 288 " ideal model delta sigma weight residual 116.34 111.55 4.79 1.40e+00 5.10e-01 1.17e+01 angle pdb=" N ASP C 187 " pdb=" CA ASP C 187 " pdb=" C ASP C 187 " ideal model delta sigma weight residual 113.18 109.41 3.77 1.33e+00 5.65e-01 8.04e+00 angle pdb=" N ASP A 380 " pdb=" CA ASP A 380 " pdb=" CB ASP A 380 " ideal model delta sigma weight residual 113.65 109.84 3.81 1.47e+00 4.63e-01 6.72e+00 angle pdb=" C3' U V 17 " pdb=" O3' U V 17 " pdb=" P C V 18 " ideal model delta sigma weight residual 120.20 123.61 -3.41 1.50e+00 4.44e-01 5.17e+00 angle pdb=" N CYS C 146 " pdb=" CA CYS C 146 " pdb=" C CYS C 146 " ideal model delta sigma weight residual 113.18 110.43 2.75 1.21e+00 6.83e-01 5.15e+00 ... (remaining 41430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.87: 10198 28.87 - 57.74: 565 57.74 - 86.61: 88 86.61 - 115.48: 6 115.48 - 144.35: 3 Dihedral angle restraints: 10860 sinusoidal: 6271 harmonic: 4589 Sorted by residual: dihedral pdb=" C4' U V 17 " pdb=" C3' U V 17 " pdb=" O3' U V 17 " pdb=" P C V 18 " ideal model delta sinusoidal sigma weight residual -110.00 11.04 -121.04 1 3.50e+01 8.16e-04 1.19e+01 dihedral pdb=" CA ASP B 406 " pdb=" CB ASP B 406 " pdb=" CG ASP B 406 " pdb=" OD1 ASP B 406 " ideal model delta sinusoidal sigma weight residual -30.00 -88.98 58.98 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" C4' A V 29 " pdb=" C3' A V 29 " pdb=" O3' A V 29 " pdb=" P G V 30 " ideal model delta sinusoidal sigma weight residual -110.00 2.88 -112.88 1 3.50e+01 8.16e-04 1.09e+01 ... (remaining 10857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1162 0.027 - 0.053: 498 0.053 - 0.080: 89 0.080 - 0.107: 59 0.107 - 0.134: 37 Chirality restraints: 1845 Sorted by residual: chirality pdb=" CA VAL C 112 " pdb=" N VAL C 112 " pdb=" C VAL C 112 " pdb=" CB VAL C 112 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA VAL A 252 " pdb=" N VAL A 252 " pdb=" C VAL A 252 " pdb=" CB VAL A 252 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1842 not shown) Planarity restraints: 3252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 161 " -0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 162 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 141 " -0.109 9.50e-02 1.11e+02 3.66e-02 1.66e+00 pdb=" NE ARG A 141 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 141 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 141 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 141 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 141 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 141 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 141 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 141 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 60 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 61 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " -0.017 5.00e-02 4.00e+02 ... (remaining 3249 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1558 2.20 - 2.80: 45940 2.80 - 3.40: 62293 3.40 - 4.00: 84193 4.00 - 4.60: 129077 Nonbonded interactions: 323061 Sorted by model distance: nonbonded pdb=" H ASN C 299 " pdb=" OE2 GLU C 364 " model vdw 1.599 2.450 nonbonded pdb="HH12 ARG A 372 " pdb=" O GLY B 7 " model vdw 1.601 2.450 nonbonded pdb=" O LEU A 215 " pdb=" HH TYR A 403 " model vdw 1.605 2.450 nonbonded pdb=" OP2 U V 37 " pdb="HO2' U V 38 " model vdw 1.612 2.450 nonbonded pdb="HH22 ARG C 11 " pdb=" OE2 GLU C 18 " model vdw 1.643 2.450 ... (remaining 323056 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 33.060 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 0.046 11885 Z= 0.114 Angle : 0.497 18.434 16259 Z= 0.243 Chirality : 0.036 0.134 1845 Planarity : 0.003 0.048 1937 Dihedral : 18.088 144.349 4710 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.34 % Favored : 96.51 % Rotamer: Outliers : 0.09 % Allowed : 15.71 % Favored : 84.21 % 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 aren not related in a simple way. whole: 1.13 (0.24), residues: 1348 helix: 2.10 (0.24), residues: 526 sheet: -0.65 (0.42), residues: 147 loop : 0.07 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 141 TYR 0.008 0.001 TYR A 403 PHE 0.009 0.001 PHE C 44 TRP 0.004 0.001 TRP C 239 HIS 0.002 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00257 (11873) covalent geometry : angle 0.45719 (16251) hydrogen bonds : bond 0.11681 ( 487) hydrogen bonds : angle 5.51974 ( 1366) metal coordination : bond 0.01458 ( 12) metal coordination : angle 8.82890 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 ARG cc_start: 0.8417 (mtp-110) cc_final: 0.8171 (ttp80) outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.4574 time to fit residues: 63.9094 Evaluate side-chains 111 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103596 restraints weight = 41829.347| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.87 r_work: 0.2948 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11885 Z= 0.176 Angle : 0.509 11.592 16259 Z= 0.253 Chirality : 0.037 0.148 1845 Planarity : 0.004 0.042 1937 Dihedral : 14.556 145.048 2139 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.01 % Favored : 95.85 % Rotamer: Outliers : 1.03 % Allowed : 14.94 % Favored : 84.03 % 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 aren not related in a simple way. whole: 0.88 (0.24), residues: 1348 helix: 1.96 (0.24), residues: 529 sheet: -0.88 (0.41), residues: 149 loop : -0.13 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 256 TYR 0.010 0.001 TYR A 403 PHE 0.009 0.001 PHE C 44 TRP 0.007 0.001 TRP C 239 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00407 (11873) covalent geometry : angle 0.48669 (16251) hydrogen bonds : bond 0.03849 ( 487) hydrogen bonds : angle 4.50824 ( 1366) metal coordination : bond 0.01172 ( 12) metal coordination : angle 6.74259 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 LEU cc_start: 0.8763 (mt) cc_final: 0.8469 (mt) outliers start: 12 outliers final: 7 residues processed: 121 average time/residue: 0.4388 time to fit residues: 67.1035 Evaluate side-chains 117 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 264 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 103 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 218 ASN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.131415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.104052 restraints weight = 41538.576| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.88 r_work: 0.3009 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11885 Z= 0.136 Angle : 0.492 12.895 16259 Z= 0.242 Chirality : 0.037 0.164 1845 Planarity : 0.004 0.060 1937 Dihedral : 14.076 144.716 2139 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.86 % Favored : 95.99 % Rotamer: Outliers : 1.03 % Allowed : 14.68 % Favored : 84.29 % 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 aren not related in a simple way. whole: 0.92 (0.24), residues: 1348 helix: 2.01 (0.24), residues: 529 sheet: -0.80 (0.41), residues: 147 loop : -0.14 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 141 TYR 0.009 0.001 TYR A 403 PHE 0.009 0.001 PHE C 44 TRP 0.007 0.001 TRP C 239 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00316 (11873) covalent geometry : angle 0.46721 (16251) hydrogen bonds : bond 0.03525 ( 487) hydrogen bonds : angle 4.26783 ( 1366) metal coordination : bond 0.01029 ( 12) metal coordination : angle 6.99257 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASP cc_start: 0.8309 (t0) cc_final: 0.7873 (t0) REVERT: B 63 ARG cc_start: 0.7798 (mtt-85) cc_final: 0.7588 (mmt90) REVERT: B 159 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8432 (mt) REVERT: C 59 LEU cc_start: 0.8805 (mt) cc_final: 0.8501 (mt) REVERT: C 389 ARG cc_start: 0.8384 (mmt180) cc_final: 0.8080 (mmt180) outliers start: 12 outliers final: 5 residues processed: 124 average time/residue: 0.4523 time to fit residues: 70.8499 Evaluate side-chains 116 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 264 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 99 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN B 378 HIS B 506 ASN C 28 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.103667 restraints weight = 41833.160| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.87 r_work: 0.3005 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11885 Z= 0.142 Angle : 0.484 12.804 16259 Z= 0.237 Chirality : 0.037 0.143 1845 Planarity : 0.004 0.074 1937 Dihedral : 14.008 144.070 2139 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 1.20 % Allowed : 14.68 % Favored : 84.12 % 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 aren not related in a simple way. whole: 0.87 (0.24), residues: 1348 helix: 2.02 (0.24), residues: 531 sheet: -0.97 (0.41), residues: 149 loop : -0.17 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 141 TYR 0.009 0.001 TYR A 403 PHE 0.011 0.001 PHE C 161 TRP 0.007 0.001 TRP C 239 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00332 (11873) covalent geometry : angle 0.45825 (16251) hydrogen bonds : bond 0.03357 ( 487) hydrogen bonds : angle 4.15723 ( 1366) metal coordination : bond 0.01022 ( 12) metal coordination : angle 7.03790 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASP cc_start: 0.8295 (t0) cc_final: 0.7828 (t0) REVERT: B 159 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8469 (mt) REVERT: C 59 LEU cc_start: 0.8819 (mt) cc_final: 0.8506 (mt) REVERT: C 389 ARG cc_start: 0.8312 (mmt180) cc_final: 0.7984 (mmt180) outliers start: 14 outliers final: 10 residues processed: 130 average time/residue: 0.4162 time to fit residues: 68.9944 Evaluate side-chains 121 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 342 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 73 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.101177 restraints weight = 41602.278| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.00 r_work: 0.3044 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11885 Z= 0.171 Angle : 0.496 12.700 16259 Z= 0.245 Chirality : 0.037 0.148 1845 Planarity : 0.004 0.068 1937 Dihedral : 14.021 143.231 2139 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.70 % Rotamer: Outliers : 1.29 % Allowed : 14.85 % Favored : 83.86 % 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 aren not related in a simple way. whole: 0.77 (0.24), residues: 1348 helix: 1.91 (0.24), residues: 531 sheet: -0.99 (0.41), residues: 147 loop : -0.23 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 141 TYR 0.009 0.001 TYR A 403 PHE 0.010 0.001 PHE C 161 TRP 0.008 0.001 TRP C 239 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00400 (11873) covalent geometry : angle 0.47129 (16251) hydrogen bonds : bond 0.03512 ( 487) hydrogen bonds : angle 4.17608 ( 1366) metal coordination : bond 0.01227 ( 12) metal coordination : angle 6.93475 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASP cc_start: 0.8325 (t0) cc_final: 0.7968 (t0) REVERT: B 159 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8578 (mt) REVERT: C 59 LEU cc_start: 0.8973 (mt) cc_final: 0.8651 (mt) REVERT: C 389 ARG cc_start: 0.8368 (mmt180) cc_final: 0.8044 (mmt180) outliers start: 15 outliers final: 11 residues processed: 123 average time/residue: 0.4228 time to fit residues: 65.7262 Evaluate side-chains 119 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 342 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 0.0670 chunk 73 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.130966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.102446 restraints weight = 41883.535| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.01 r_work: 0.3059 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11885 Z= 0.122 Angle : 0.475 12.755 16259 Z= 0.233 Chirality : 0.036 0.144 1845 Planarity : 0.004 0.074 1937 Dihedral : 13.958 142.804 2139 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.08 % Favored : 95.85 % Rotamer: Outliers : 1.37 % Allowed : 14.76 % Favored : 83.86 % 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 aren not related in a simple way. whole: 0.86 (0.24), residues: 1348 helix: 2.01 (0.24), residues: 531 sheet: -1.00 (0.41), residues: 147 loop : -0.18 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 141 TYR 0.008 0.001 TYR A 403 PHE 0.009 0.001 PHE C 44 TRP 0.007 0.001 TRP C 239 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00284 (11873) covalent geometry : angle 0.44999 (16251) hydrogen bonds : bond 0.03210 ( 487) hydrogen bonds : angle 4.06163 ( 1366) metal coordination : bond 0.00980 ( 12) metal coordination : angle 6.89614 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASP cc_start: 0.8296 (t0) cc_final: 0.7861 (t70) REVERT: B 159 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8562 (mt) REVERT: C 59 LEU cc_start: 0.8963 (mt) cc_final: 0.8640 (mt) REVERT: C 343 ASP cc_start: 0.8455 (t0) cc_final: 0.8148 (t0) REVERT: C 389 ARG cc_start: 0.8365 (mmt180) cc_final: 0.8025 (mmt180) outliers start: 16 outliers final: 13 residues processed: 127 average time/residue: 0.4249 time to fit residues: 68.4474 Evaluate side-chains 122 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 342 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 46 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 75 ASN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.128969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100301 restraints weight = 41899.722| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.01 r_work: 0.3025 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11885 Z= 0.205 Angle : 0.519 13.712 16259 Z= 0.256 Chirality : 0.038 0.148 1845 Planarity : 0.004 0.082 1937 Dihedral : 14.035 141.122 2139 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.60 % Favored : 95.33 % Rotamer: Outliers : 1.63 % Allowed : 14.94 % Favored : 83.43 % 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 aren not related in a simple way. whole: 0.61 (0.24), residues: 1348 helix: 1.80 (0.23), residues: 531 sheet: -1.19 (0.40), residues: 149 loop : -0.30 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 141 TYR 0.010 0.001 TYR A 403 PHE 0.012 0.001 PHE C 161 TRP 0.008 0.001 TRP C 239 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00482 (11873) covalent geometry : angle 0.49205 (16251) hydrogen bonds : bond 0.03733 ( 487) hydrogen bonds : angle 4.22811 ( 1366) metal coordination : bond 0.01502 ( 12) metal coordination : angle 7.43333 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASP cc_start: 0.8348 (t0) cc_final: 0.7887 (t70) REVERT: B 148 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: B 159 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8654 (mt) REVERT: C 59 LEU cc_start: 0.8973 (mt) cc_final: 0.8643 (mt) REVERT: C 343 ASP cc_start: 0.8494 (t0) cc_final: 0.8216 (t0) REVERT: C 389 ARG cc_start: 0.8376 (mmt180) cc_final: 0.8005 (mmt180) outliers start: 19 outliers final: 16 residues processed: 123 average time/residue: 0.4044 time to fit residues: 62.9690 Evaluate side-chains 125 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 342 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.132680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.104459 restraints weight = 42797.407| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.96 r_work: 0.3100 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11885 Z= 0.166 Angle : 0.498 12.580 16259 Z= 0.247 Chirality : 0.037 0.144 1845 Planarity : 0.004 0.081 1937 Dihedral : 14.009 140.786 2139 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 1.37 % Allowed : 15.45 % Favored : 83.18 % 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 aren not related in a simple way. whole: 0.65 (0.24), residues: 1348 helix: 1.83 (0.24), residues: 531 sheet: -1.12 (0.41), residues: 147 loop : -0.30 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 141 TYR 0.009 0.001 TYR A 403 PHE 0.011 0.001 PHE C 161 TRP 0.008 0.001 TRP C 239 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00387 (11873) covalent geometry : angle 0.47428 (16251) hydrogen bonds : bond 0.03511 ( 487) hydrogen bonds : angle 4.17655 ( 1366) metal coordination : bond 0.01193 ( 12) metal coordination : angle 6.84727 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASP cc_start: 0.8268 (t0) cc_final: 0.7885 (t70) REVERT: B 159 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8712 (mt) REVERT: C 59 LEU cc_start: 0.9058 (mt) cc_final: 0.8729 (mt) REVERT: C 343 ASP cc_start: 0.8532 (t0) cc_final: 0.8285 (t0) REVERT: C 346 LYS cc_start: 0.8157 (mttt) cc_final: 0.7891 (mttt) REVERT: C 389 ARG cc_start: 0.8395 (mmt180) cc_final: 0.8037 (mmt180) outliers start: 16 outliers final: 14 residues processed: 121 average time/residue: 0.3866 time to fit residues: 58.8520 Evaluate side-chains 119 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 342 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 59 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.106206 restraints weight = 42902.344| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.97 r_work: 0.3127 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11885 Z= 0.116 Angle : 0.469 11.084 16259 Z= 0.233 Chirality : 0.036 0.138 1845 Planarity : 0.004 0.078 1937 Dihedral : 13.917 140.580 2139 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.03 % Allowed : 15.79 % Favored : 83.18 % 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 aren not related in a simple way. whole: 0.79 (0.24), residues: 1348 helix: 2.00 (0.24), residues: 531 sheet: -1.12 (0.41), residues: 147 loop : -0.24 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 141 TYR 0.008 0.001 TYR A 403 PHE 0.009 0.001 PHE C 161 TRP 0.008 0.001 TRP C 239 HIS 0.003 0.001 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.00271 (11873) covalent geometry : angle 0.45002 (16251) hydrogen bonds : bond 0.03162 ( 487) hydrogen bonds : angle 4.05240 ( 1366) metal coordination : bond 0.00884 ( 12) metal coordination : angle 6.04505 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASP cc_start: 0.8230 (t0) cc_final: 0.7814 (t70) REVERT: B 159 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8662 (mt) REVERT: C 59 LEU cc_start: 0.9035 (mt) cc_final: 0.8711 (mt) REVERT: C 111 ARG cc_start: 0.7220 (ptp90) cc_final: 0.6867 (ptt-90) REVERT: C 343 ASP cc_start: 0.8512 (t0) cc_final: 0.8255 (t0) REVERT: C 346 LYS cc_start: 0.8163 (mttt) cc_final: 0.7896 (mttt) REVERT: C 358 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7148 (mm-30) REVERT: C 389 ARG cc_start: 0.8410 (mmt180) cc_final: 0.8062 (mmt180) outliers start: 12 outliers final: 11 residues processed: 115 average time/residue: 0.4360 time to fit residues: 63.6362 Evaluate side-chains 116 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 342 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 89 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 0.0980 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.106979 restraints weight = 42965.341| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.97 r_work: 0.3137 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11885 Z= 0.104 Angle : 0.463 10.431 16259 Z= 0.230 Chirality : 0.036 0.139 1845 Planarity : 0.004 0.077 1937 Dihedral : 13.881 139.756 2139 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.12 % Allowed : 15.79 % Favored : 83.09 % 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 aren not related in a simple way. whole: 0.85 (0.24), residues: 1348 helix: 2.00 (0.24), residues: 539 sheet: -1.15 (0.41), residues: 149 loop : -0.17 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 141 TYR 0.008 0.001 TYR A 403 PHE 0.008 0.001 PHE C 161 TRP 0.005 0.001 TRP A 346 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00243 (11873) covalent geometry : angle 0.44473 (16251) hydrogen bonds : bond 0.03052 ( 487) hydrogen bonds : angle 3.99010 ( 1366) metal coordination : bond 0.00829 ( 12) metal coordination : angle 5.75217 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASP cc_start: 0.8220 (t0) cc_final: 0.7853 (t70) REVERT: B 159 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8679 (mt) REVERT: C 59 LEU cc_start: 0.9039 (mt) cc_final: 0.8715 (mt) REVERT: C 111 ARG cc_start: 0.7227 (ptp90) cc_final: 0.6852 (ptt-90) REVERT: C 187 ASP cc_start: 0.6059 (t0) cc_final: 0.5797 (t0) REVERT: C 343 ASP cc_start: 0.8516 (t0) cc_final: 0.8259 (t0) REVERT: C 346 LYS cc_start: 0.8173 (mttt) cc_final: 0.7910 (mttt) REVERT: C 389 ARG cc_start: 0.8407 (mmt180) cc_final: 0.8062 (mmt180) outliers start: 13 outliers final: 11 residues processed: 119 average time/residue: 0.4449 time to fit residues: 67.2232 Evaluate side-chains 120 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 342 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 3 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 97 optimal weight: 0.2980 chunk 112 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.134550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.105939 restraints weight = 42446.072| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.02 r_work: 0.3120 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11885 Z= 0.102 Angle : 0.490 16.728 16259 Z= 0.230 Chirality : 0.036 0.140 1845 Planarity : 0.004 0.076 1937 Dihedral : 13.849 139.024 2139 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.03 % Allowed : 15.88 % Favored : 83.09 % 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 aren not related in a simple way. whole: 0.91 (0.24), residues: 1348 helix: 2.06 (0.24), residues: 539 sheet: -1.14 (0.41), residues: 149 loop : -0.14 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 141 TYR 0.008 0.001 TYR A 403 PHE 0.010 0.001 PHE C 161 TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.00240 (11873) covalent geometry : angle 0.44105 (16251) hydrogen bonds : bond 0.03006 ( 487) hydrogen bonds : angle 3.95865 ( 1366) metal coordination : bond 0.00918 ( 12) metal coordination : angle 9.63206 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5616.61 seconds wall clock time: 96 minutes 15.23 seconds (5775.23 seconds total)