Starting phenix.real_space_refine on Thu Sep 18 02:47:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ip3_60756/09_2025/9ip3_60756.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ip3_60756/09_2025/9ip3_60756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ip3_60756/09_2025/9ip3_60756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ip3_60756/09_2025/9ip3_60756.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ip3_60756/09_2025/9ip3_60756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ip3_60756/09_2025/9ip3_60756.map" } resolution = 3.1 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= 0.001 sd= 0.078 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 79 5.16 5 C 8613 2.51 5 N 2289 2.21 5 O 2482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13464 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1365, 10948 Classifications: {'peptide': 1365} Link IDs: {'PCIS': 2, 'PTRANS': 70, 'TRANS': 1292} Chain breaks: 3 Chain: "B" Number of atoms: 1684 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 1677 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 201} Conformer: "B" Number of residues, atoms: 218, 1677 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 201} bond proxies already assigned to first conformer: 1704 Chain: "C" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 417 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "D" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 231 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "E" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 183 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9137 SG CYS A1150 80.692 80.049 25.267 1.00 50.25 S ATOM 9159 SG CYS A1153 81.704 83.492 26.350 1.00 79.12 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATHR B 335 " occ=0.42 ... (12 atoms not shown) pdb=" CG2BTHR B 335 " occ=0.58 Time building chain proxies: 3.66, per 1000 atoms: 0.27 Number of scatterers: 13464 At special positions: 0 Unit cell: (99.51, 123.69, 122.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 79 16.00 O 2482 8.00 N 2289 7.00 C 8613 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1105 " - pdb=" SG CYS A1352 " distance=2.05 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: 1.23 Conformation dependent library (CDL) restraints added in 659.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" ND1 HIS A1345 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A1347 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1150 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1153 " Number of angles added : 2 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 9 sheets defined 59.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.546A pdb=" N ARG A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 removed outlier: 4.035A pdb=" N ASN A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.983A pdb=" N ARG A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.779A pdb=" N THR A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 84 removed outlier: 3.622A pdb=" N ILE A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 95 through 122 removed outlier: 4.118A pdb=" N PHE A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 100 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 145 through 165 Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.636A pdb=" N SER A 171 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR A 172 " --> pdb=" O SER A 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 172' Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 206 through 213 removed outlier: 3.523A pdb=" N MET A 210 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 234 through 261 Processing helix chain 'A' and resid 269 through 288 Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 313 through 336 removed outlier: 3.688A pdb=" N GLY A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 349 removed outlier: 3.872A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 361 through 369 Processing helix chain 'A' and resid 370 through 376 removed outlier: 5.882A pdb=" N LYS A 373 " --> pdb=" O SER A 370 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP A 375 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 removed outlier: 3.911A pdb=" N LYS A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 424 Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.790A pdb=" N TYR A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.630A pdb=" N LEU A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.679A pdb=" N ILE A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 498 removed outlier: 5.762A pdb=" N ASP A 495 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 497 " --> pdb=" O TRP A 494 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 498 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 515 through 523 Processing helix chain 'A' and resid 527 through 537 Processing helix chain 'A' and resid 538 through 546 Proline residue: A 543 - end of helix Processing helix chain 'A' and resid 567 through 584 Processing helix chain 'A' and resid 585 through 589 Processing helix chain 'A' and resid 601 through 609 Processing helix chain 'A' and resid 635 through 640 removed outlier: 3.857A pdb=" N ALA A 639 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 Proline residue: A 647 - end of helix Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 712 through 732 Processing helix chain 'A' and resid 757 through 784 Processing helix chain 'A' and resid 815 through 820 Processing helix chain 'A' and resid 832 through 850 Processing helix chain 'A' and resid 854 through 875 Processing helix chain 'A' and resid 884 through 891 removed outlier: 3.632A pdb=" N THR A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 890 " --> pdb=" O GLY A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 927 through 943 Processing helix chain 'A' and resid 945 through 947 No H-bonds generated for 'chain 'A' and resid 945 through 947' Processing helix chain 'A' and resid 948 through 954 Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'A' and resid 980 through 996 Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1008 through 1021 Processing helix chain 'A' and resid 1027 through 1036 Processing helix chain 'A' and resid 1038 through 1048 Processing helix chain 'A' and resid 1052 through 1059 Processing helix chain 'A' and resid 1069 through 1087 Processing helix chain 'A' and resid 1093 through 1100 Processing helix chain 'A' and resid 1105 through 1118 Processing helix chain 'A' and resid 1118 through 1123 Processing helix chain 'A' and resid 1134 through 1138 Processing helix chain 'A' and resid 1150 through 1156 removed outlier: 3.558A pdb=" N ALA A1156 " --> pdb=" O GLN A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1184 No H-bonds generated for 'chain 'A' and resid 1182 through 1184' Processing helix chain 'A' and resid 1213 through 1230 Processing helix chain 'A' and resid 1235 through 1246 Proline residue: A1242 - end of helix Processing helix chain 'A' and resid 1251 through 1259 Processing helix chain 'A' and resid 1266 through 1274 removed outlier: 3.918A pdb=" N GLN A1274 " --> pdb=" O ARG A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1303 removed outlier: 3.553A pdb=" N GLY A1300 " --> pdb=" O ASN A1297 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU A1301 " --> pdb=" O THR A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1331 Processing helix chain 'A' and resid 1335 through 1339 Processing helix chain 'A' and resid 1350 through 1353 removed outlier: 3.508A pdb=" N THR A1353 " --> pdb=" O LYS A1350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1350 through 1353' Processing helix chain 'A' and resid 1370 through 1376 removed outlier: 3.535A pdb=" N ARG A1373 " --> pdb=" O ASP A1370 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU A1376 " --> pdb=" O ARG A1373 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 149 Processing helix chain 'B' and resid 155 through 166 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 193 through 206 removed outlier: 3.698A pdb=" N THR B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 220 through 232 removed outlier: 3.840A pdb=" N HIS B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 254 removed outlier: 3.504A pdb=" N GLN B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 269 Processing helix chain 'B' and resid 272 through 284 removed outlier: 3.735A pdb=" N VAL B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 288 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'C' and resid 125 through 144 removed outlier: 3.678A pdb=" N ASP C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 Processing helix chain 'D' and resid 121 through 146 removed outlier: 3.520A pdb=" N LEU D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 133 Processing helix chain 'E' and resid 134 through 146 removed outlier: 3.617A pdb=" N LEU E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 194 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA3, first strand: chain 'A' and resid 549 through 550 Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 740 removed outlier: 3.513A pdb=" N VAL A 630 " --> pdb=" O PHE A 793 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE A 793 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 799 Processing sheet with id=AA6, first strand: chain 'A' and resid 1139 through 1144 removed outlier: 3.717A pdb=" N ARG A1343 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1175 through 1176 Processing sheet with id=AA8, first strand: chain 'A' and resid 1208 through 1209 removed outlier: 3.778A pdb=" N LYS A1208 " --> pdb=" O ASN A1391 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 311 through 313 667 hydrogen bonds defined for protein. 1903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4213 1.34 - 1.47: 3496 1.47 - 1.60: 5956 1.60 - 1.72: 1 1.72 - 1.85: 116 Bond restraints: 13782 Sorted by residual: bond pdb=" CG TYR A1381 " pdb=" CD2 TYR A1381 " ideal model delta sigma weight residual 1.389 1.497 -0.108 2.10e-02 2.27e+03 2.66e+01 bond pdb=" CA PRO C 169 " pdb=" C PRO C 169 " ideal model delta sigma weight residual 1.517 1.470 0.047 9.30e-03 1.16e+04 2.51e+01 bond pdb=" CB TRP A1085 " pdb=" CG TRP A1085 " ideal model delta sigma weight residual 1.498 1.366 0.132 3.10e-02 1.04e+03 1.80e+01 bond pdb=" CB TYR A 188 " pdb=" CG TYR A 188 " ideal model delta sigma weight residual 1.512 1.429 0.083 2.20e-02 2.07e+03 1.42e+01 bond pdb=" CA PRO A 694 " pdb=" C PRO A 694 " ideal model delta sigma weight residual 1.514 1.535 -0.021 5.50e-03 3.31e+04 1.42e+01 ... (remaining 13777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 18180 3.20 - 6.41: 470 6.41 - 9.61: 50 9.61 - 12.82: 10 12.82 - 16.02: 1 Bond angle restraints: 18711 Sorted by residual: angle pdb=" N TYR A1381 " pdb=" CA TYR A1381 " pdb=" C TYR A1381 " ideal model delta sigma weight residual 109.31 100.82 8.49 1.42e+00 4.96e-01 3.57e+01 angle pdb=" C ILE A1380 " pdb=" N TYR A1381 " pdb=" CA TYR A1381 " ideal model delta sigma weight residual 122.15 113.31 8.84 1.74e+00 3.30e-01 2.58e+01 angle pdb=" N ILE A 829 " pdb=" CA ILE A 829 " pdb=" C ILE A 829 " ideal model delta sigma weight residual 109.30 103.49 5.81 1.25e+00 6.40e-01 2.16e+01 angle pdb=" CA LEU A 972 " pdb=" CB LEU A 972 " pdb=" CG LEU A 972 " ideal model delta sigma weight residual 116.30 100.28 16.02 3.50e+00 8.16e-02 2.10e+01 angle pdb=" NE ARG A 318 " pdb=" CZ ARG A 318 " pdb=" NH2 ARG A 318 " ideal model delta sigma weight residual 119.20 123.29 -4.09 9.00e-01 1.23e+00 2.06e+01 ... (remaining 18706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 7815 17.73 - 35.46: 423 35.46 - 53.19: 65 53.19 - 70.92: 12 70.92 - 88.65: 7 Dihedral angle restraints: 8322 sinusoidal: 3341 harmonic: 4981 Sorted by residual: dihedral pdb=" CB CYS A1105 " pdb=" SG CYS A1105 " pdb=" SG CYS A1352 " pdb=" CB CYS A1352 " ideal model delta sinusoidal sigma weight residual 93.00 142.47 -49.47 1 1.00e+01 1.00e-02 3.36e+01 dihedral pdb=" CA TYR A1381 " pdb=" C TYR A1381 " pdb=" N ASP A1382 " pdb=" CA ASP A1382 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA ASN A 663 " pdb=" C ASN A 663 " pdb=" N TRP A 664 " pdb=" CA TRP A 664 " ideal model delta harmonic sigma weight residual 180.00 -155.81 -24.19 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 8319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 2006 0.125 - 0.249: 94 0.249 - 0.374: 7 0.374 - 0.499: 1 0.499 - 0.624: 1 Chirality restraints: 2109 Sorted by residual: chirality pdb=" CG LEU A 396 " pdb=" CB LEU A 396 " pdb=" CD1 LEU A 396 " pdb=" CD2 LEU A 396 " both_signs ideal model delta sigma weight residual False -2.59 -3.21 0.62 2.00e-01 2.50e+01 9.72e+00 chirality pdb=" CB ILE A 799 " pdb=" CA ILE A 799 " pdb=" CG1 ILE A 799 " pdb=" CG2 ILE A 799 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB ILE A 73 " pdb=" CA ILE A 73 " pdb=" CG1 ILE A 73 " pdb=" CG2 ILE A 73 " both_signs ideal model delta sigma weight residual False 2.64 3.00 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 2106 not shown) Planarity restraints: 2391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 867 " 0.048 2.00e-02 2.50e+03 4.98e-02 4.34e+01 pdb=" CG PHE A 867 " -0.115 2.00e-02 2.50e+03 pdb=" CD1 PHE A 867 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE A 867 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 867 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 867 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE A 867 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 319 " 0.013 2.00e-02 2.50e+03 4.68e-02 3.84e+01 pdb=" CG PHE A 319 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 PHE A 319 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 319 " 0.074 2.00e-02 2.50e+03 pdb=" CE1 PHE A 319 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE A 319 " -0.031 2.00e-02 2.50e+03 pdb=" CZ PHE A 319 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1381 " 0.035 2.00e-02 2.50e+03 4.07e-02 3.32e+01 pdb=" CG TYR A1381 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TYR A1381 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A1381 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A1381 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR A1381 " 0.056 2.00e-02 2.50e+03 pdb=" CZ TYR A1381 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1381 " -0.030 2.00e-02 2.50e+03 ... (remaining 2388 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2319 2.75 - 3.29: 14159 3.29 - 3.83: 22787 3.83 - 4.36: 28246 4.36 - 4.90: 47193 Nonbonded interactions: 114704 Sorted by model distance: nonbonded pdb=" O LEU A1021 " pdb=" NH2 ARG A1125 " model vdw 2.213 3.120 nonbonded pdb=" OE2 GLU A 643 " pdb=" OG1 THR C 153 " model vdw 2.213 3.040 nonbonded pdb=" NH1 ARG B 300 " pdb=" OE1 GLN B 308 " model vdw 2.225 3.120 nonbonded pdb=" OG1 THR B 159 " pdb=" OG SER B 174 " model vdw 2.240 3.040 nonbonded pdb=" O GLU A1148 " pdb=" NH2 ARG A1343 " model vdw 2.240 3.120 ... (remaining 114699 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=0.42 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.710 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 : 0.012 0.147 13787 Z= 0.632 Angle : 1.220 16.024 18715 Z= 0.661 Chirality : 0.065 0.624 2109 Planarity : 0.006 0.050 2391 Dihedral : 11.484 88.645 5091 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.14 (0.19), residues: 1680 helix: -0.65 (0.16), residues: 879 sheet: -1.46 (0.44), residues: 107 loop : -0.54 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A1081 TYR 0.082 0.005 TYR A1381 PHE 0.115 0.005 PHE A 867 TRP 0.030 0.004 TRP A 664 HIS 0.018 0.004 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.01238 (13782) covalent geometry : angle 1.21701 (18711) SS BOND : bond 0.01522 ( 1) SS BOND : angle 0.76624 ( 2) hydrogen bonds : bond 0.16790 ( 667) hydrogen bonds : angle 7.10059 ( 1903) metal coordination : bond 0.09014 ( 4) metal coordination : angle 8.71570 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 LYS cc_start: 0.8593 (tttp) cc_final: 0.8080 (mtmm) REVERT: A 332 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7909 (mt-10) REVERT: A 470 PHE cc_start: 0.8771 (m-80) cc_final: 0.8482 (m-80) REVERT: A 514 LYS cc_start: 0.7800 (ptpt) cc_final: 0.7365 (pttt) REVERT: A 518 GLU cc_start: 0.8715 (tt0) cc_final: 0.8084 (mt-10) REVERT: A 533 SER cc_start: 0.8972 (m) cc_final: 0.8634 (p) REVERT: A 713 GLN cc_start: 0.8019 (tp40) cc_final: 0.7537 (tt0) REVERT: A 740 MET cc_start: 0.7955 (tpp) cc_final: 0.7648 (mtt) REVERT: A 1217 ARG cc_start: 0.7455 (ttm110) cc_final: 0.6966 (ttp80) REVERT: B 188 ARG cc_start: 0.6426 (mmp80) cc_final: 0.5686 (tpt90) REVERT: B 244 GLN cc_start: 0.8837 (pt0) cc_final: 0.8524 (pt0) REVERT: C 124 MET cc_start: 0.4362 (mmp) cc_final: 0.4108 (mmm) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.1479 time to fit residues: 66.6706 Evaluate side-chains 211 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 165 ASN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 HIS A 808 ASN A 876 HIS A 924 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.167113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134180 restraints weight = 35032.803| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.84 r_work: 0.3334 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13787 Z= 0.147 Angle : 0.612 9.299 18715 Z= 0.307 Chirality : 0.042 0.163 2109 Planarity : 0.004 0.044 2391 Dihedral : 4.562 21.694 1836 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.41 % Allowed : 7.76 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.30 (0.21), residues: 1680 helix: 0.67 (0.18), residues: 896 sheet: -1.08 (0.45), residues: 105 loop : -0.04 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 182 TYR 0.017 0.001 TYR A 106 PHE 0.029 0.002 PHE A 867 TRP 0.017 0.001 TRP A1019 HIS 0.005 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00347 (13782) covalent geometry : angle 0.61003 (18711) SS BOND : bond 0.00066 ( 1) SS BOND : angle 1.93364 ( 2) hydrogen bonds : bond 0.04391 ( 667) hydrogen bonds : angle 4.95092 ( 1903) metal coordination : bond 0.01222 ( 4) metal coordination : angle 4.00284 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8585 (ttpp) REVERT: A 214 GLN cc_start: 0.8115 (tt0) cc_final: 0.7425 (mm-40) REVERT: A 271 LYS cc_start: 0.8563 (tttp) cc_final: 0.8068 (mtmm) REVERT: A 444 LYS cc_start: 0.8244 (mtpp) cc_final: 0.8036 (mtmt) REVERT: A 453 MET cc_start: 0.7827 (tpt) cc_final: 0.7538 (tpt) REVERT: A 514 LYS cc_start: 0.7575 (ptpt) cc_final: 0.7043 (pttt) REVERT: A 518 GLU cc_start: 0.8117 (tt0) cc_final: 0.7668 (mt-10) REVERT: A 532 LEU cc_start: 0.8434 (mt) cc_final: 0.8198 (tp) REVERT: A 999 LYS cc_start: 0.8003 (tppt) cc_final: 0.7623 (mttm) REVERT: A 1015 MET cc_start: 0.8156 (mmm) cc_final: 0.7876 (mmp) REVERT: A 1217 ARG cc_start: 0.7109 (ttm110) cc_final: 0.6669 (ttp80) REVERT: B 188 ARG cc_start: 0.6178 (mmp80) cc_final: 0.5360 (tpt90) REVERT: B 202 ASN cc_start: 0.8873 (m110) cc_final: 0.8399 (m110) REVERT: C 177 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8303 (mm-30) outliers start: 21 outliers final: 11 residues processed: 245 average time/residue: 0.1406 time to fit residues: 48.3776 Evaluate side-chains 205 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 86 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 44 optimal weight: 0.0050 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 HIS A 608 GLN A 663 ASN ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 ASN B 244 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.171060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135560 restraints weight = 27583.218| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.11 r_work: 0.3394 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13787 Z= 0.117 Angle : 0.547 7.099 18715 Z= 0.273 Chirality : 0.040 0.163 2109 Planarity : 0.004 0.046 2391 Dihedral : 4.366 23.374 1836 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.74 % Allowed : 10.04 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.76 (0.21), residues: 1680 helix: 1.07 (0.18), residues: 895 sheet: -0.89 (0.46), residues: 105 loop : 0.15 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.016 0.001 TYR A 667 PHE 0.021 0.001 PHE A 867 TRP 0.014 0.001 TRP B 324 HIS 0.005 0.001 HIS A 607 Details of bonding type rmsd covalent geometry : bond 0.00271 (13782) covalent geometry : angle 0.54585 (18711) SS BOND : bond 0.00020 ( 1) SS BOND : angle 1.65647 ( 2) hydrogen bonds : bond 0.03715 ( 667) hydrogen bonds : angle 4.60178 ( 1903) metal coordination : bond 0.01078 ( 4) metal coordination : angle 2.74796 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 214 GLN cc_start: 0.8034 (tt0) cc_final: 0.7394 (mm-40) REVERT: A 253 ILE cc_start: 0.8526 (mt) cc_final: 0.8324 (mt) REVERT: A 271 LYS cc_start: 0.8498 (tttp) cc_final: 0.7988 (mtmm) REVERT: A 444 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7991 (mtmt) REVERT: A 514 LYS cc_start: 0.7508 (ptpt) cc_final: 0.7017 (pttt) REVERT: A 518 GLU cc_start: 0.7909 (tt0) cc_final: 0.7452 (mt-10) REVERT: A 736 ARG cc_start: 0.7916 (mmt90) cc_final: 0.7184 (mmt180) REVERT: A 999 LYS cc_start: 0.8011 (tppt) cc_final: 0.7638 (mttm) REVERT: A 1015 MET cc_start: 0.8194 (mmm) cc_final: 0.7906 (mmp) REVERT: A 1217 ARG cc_start: 0.7070 (ttm110) cc_final: 0.6650 (ttp80) REVERT: A 1280 PHE cc_start: 0.7196 (m-10) cc_final: 0.6882 (m-10) REVERT: A 1375 ARG cc_start: 0.8345 (ttm110) cc_final: 0.7667 (ttm-80) REVERT: A 1384 ASN cc_start: 0.7881 (t0) cc_final: 0.7680 (m-40) REVERT: B 148 THR cc_start: 0.7758 (p) cc_final: 0.7519 (p) REVERT: B 188 ARG cc_start: 0.6072 (mmp80) cc_final: 0.5271 (tpt90) REVERT: B 202 ASN cc_start: 0.8917 (m110) cc_final: 0.8363 (m110) REVERT: C 177 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8287 (mm-30) outliers start: 26 outliers final: 16 residues processed: 233 average time/residue: 0.1383 time to fit residues: 45.4216 Evaluate side-chains 206 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1311 ASP Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain B residue 244 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 20 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN E 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.165827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.132294 restraints weight = 35049.296| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.80 r_work: 0.3286 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13787 Z= 0.171 Angle : 0.569 7.721 18715 Z= 0.284 Chirality : 0.041 0.153 2109 Planarity : 0.004 0.045 2391 Dihedral : 4.355 23.812 1836 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.47 % Allowed : 11.38 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.82 (0.21), residues: 1680 helix: 1.10 (0.18), residues: 888 sheet: -0.90 (0.45), residues: 107 loop : 0.22 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 182 TYR 0.011 0.001 TYR A1322 PHE 0.018 0.002 PHE A 867 TRP 0.013 0.001 TRP B 324 HIS 0.006 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00421 (13782) covalent geometry : angle 0.56756 (18711) SS BOND : bond 0.00058 ( 1) SS BOND : angle 1.64523 ( 2) hydrogen bonds : bond 0.03828 ( 667) hydrogen bonds : angle 4.62392 ( 1903) metal coordination : bond 0.00803 ( 4) metal coordination : angle 3.03464 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8597 (ttmm) REVERT: A 178 ASP cc_start: 0.7952 (m-30) cc_final: 0.7150 (m-30) REVERT: A 214 GLN cc_start: 0.8100 (tt0) cc_final: 0.7375 (mm-40) REVERT: A 444 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7962 (mtmt) REVERT: A 514 LYS cc_start: 0.7608 (ptpt) cc_final: 0.7063 (pttt) REVERT: A 518 GLU cc_start: 0.7987 (tt0) cc_final: 0.7576 (mt-10) REVERT: A 736 ARG cc_start: 0.8094 (mmt90) cc_final: 0.7318 (mmt180) REVERT: A 999 LYS cc_start: 0.8029 (tppt) cc_final: 0.7687 (mttm) REVERT: A 1217 ARG cc_start: 0.7147 (ttm110) cc_final: 0.6724 (ttp80) REVERT: A 1280 PHE cc_start: 0.7323 (m-10) cc_final: 0.6972 (m-10) REVERT: A 1334 THR cc_start: 0.9097 (t) cc_final: 0.8792 (p) REVERT: A 1375 ARG cc_start: 0.8377 (ttm110) cc_final: 0.7661 (ttm-80) REVERT: A 1383 SER cc_start: 0.8036 (m) cc_final: 0.7412 (p) REVERT: A 1384 ASN cc_start: 0.7898 (t0) cc_final: 0.7671 (m-40) REVERT: B 182 ARG cc_start: 0.7741 (tpp80) cc_final: 0.7013 (ttm-80) REVERT: B 188 ARG cc_start: 0.6211 (mmp80) cc_final: 0.5322 (tpt90) REVERT: B 202 ASN cc_start: 0.8920 (m110) cc_final: 0.8289 (m110) REVERT: B 244 GLN cc_start: 0.8791 (pt0) cc_final: 0.8360 (pm20) REVERT: C 177 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8416 (mm-30) outliers start: 22 outliers final: 13 residues processed: 218 average time/residue: 0.1396 time to fit residues: 42.8844 Evaluate side-chains 201 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1311 ASP Chi-restraints excluded: chain A residue 1326 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 74 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 140 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1266 ASN B 244 GLN E 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.168969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135706 restraints weight = 28865.573| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.02 r_work: 0.3378 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13787 Z= 0.112 Angle : 0.531 9.044 18715 Z= 0.263 Chirality : 0.039 0.154 2109 Planarity : 0.004 0.045 2391 Dihedral : 4.222 24.289 1836 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.74 % Allowed : 12.45 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.01 (0.21), residues: 1680 helix: 1.24 (0.18), residues: 891 sheet: -0.88 (0.48), residues: 102 loop : 0.34 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 182 TYR 0.012 0.001 TYR A1381 PHE 0.017 0.001 PHE A 411 TRP 0.013 0.001 TRP B 324 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00265 (13782) covalent geometry : angle 0.53043 (18711) SS BOND : bond 0.00024 ( 1) SS BOND : angle 1.52518 ( 2) hydrogen bonds : bond 0.03400 ( 667) hydrogen bonds : angle 4.48262 ( 1903) metal coordination : bond 0.01176 ( 4) metal coordination : angle 2.83626 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7965 (tpm170) cc_final: 0.7708 (tpm170) REVERT: A 48 LYS cc_start: 0.8225 (mmmt) cc_final: 0.7993 (mmmt) REVERT: A 178 ASP cc_start: 0.7838 (m-30) cc_final: 0.7002 (m-30) REVERT: A 214 GLN cc_start: 0.8001 (tt0) cc_final: 0.7401 (mm110) REVERT: A 253 ILE cc_start: 0.8545 (mt) cc_final: 0.8337 (mt) REVERT: A 444 LYS cc_start: 0.8274 (mtpp) cc_final: 0.8029 (mtmt) REVERT: A 514 LYS cc_start: 0.7538 (ptpt) cc_final: 0.7032 (pttt) REVERT: A 518 GLU cc_start: 0.7771 (tt0) cc_final: 0.7398 (mt-10) REVERT: A 736 ARG cc_start: 0.7994 (mmt90) cc_final: 0.7251 (mmt180) REVERT: A 999 LYS cc_start: 0.7984 (tppt) cc_final: 0.7636 (mttm) REVERT: A 1217 ARG cc_start: 0.7041 (ttm110) cc_final: 0.6648 (ttp80) REVERT: A 1271 TYR cc_start: 0.5894 (OUTLIER) cc_final: 0.4876 (t80) REVERT: A 1280 PHE cc_start: 0.7207 (m-10) cc_final: 0.6877 (m-10) REVERT: A 1334 THR cc_start: 0.9086 (t) cc_final: 0.8772 (p) REVERT: A 1375 ARG cc_start: 0.8420 (ttm110) cc_final: 0.7579 (ttt-90) REVERT: A 1383 SER cc_start: 0.7895 (m) cc_final: 0.7225 (p) REVERT: A 1384 ASN cc_start: 0.7907 (t0) cc_final: 0.7631 (m-40) REVERT: B 148 THR cc_start: 0.7730 (p) cc_final: 0.7486 (p) REVERT: B 182 ARG cc_start: 0.7781 (tpp80) cc_final: 0.7060 (ttm-80) REVERT: B 188 ARG cc_start: 0.6141 (mmp80) cc_final: 0.5339 (tpt90) REVERT: B 202 ASN cc_start: 0.8718 (m110) cc_final: 0.8117 (m110) REVERT: C 177 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8312 (mm-30) REVERT: E 132 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7809 (m-40) outliers start: 26 outliers final: 15 residues processed: 226 average time/residue: 0.1291 time to fit residues: 41.6839 Evaluate side-chains 209 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1271 TYR Chi-restraints excluded: chain A residue 1311 ASP Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain B residue 176 TYR Chi-restraints excluded: chain E residue 132 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 12 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 89 optimal weight: 0.4980 chunk 75 optimal weight: 5.9990 chunk 95 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 ASN D 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.165572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129942 restraints weight = 26219.401| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.81 r_work: 0.3306 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 13787 Z= 0.227 Angle : 0.608 8.017 18715 Z= 0.303 Chirality : 0.043 0.175 2109 Planarity : 0.004 0.044 2391 Dihedral : 4.407 24.446 1836 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.01 % Allowed : 13.19 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.73 (0.21), residues: 1680 helix: 1.00 (0.18), residues: 890 sheet: -1.06 (0.49), residues: 102 loop : 0.23 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 197 TYR 0.014 0.002 TYR A 117 PHE 0.018 0.002 PHE A1011 TRP 0.014 0.002 TRP A 191 HIS 0.008 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00560 (13782) covalent geometry : angle 0.60709 (18711) SS BOND : bond 0.00115 ( 1) SS BOND : angle 1.64420 ( 2) hydrogen bonds : bond 0.04012 ( 667) hydrogen bonds : angle 4.68282 ( 1903) metal coordination : bond 0.00680 ( 4) metal coordination : angle 3.68157 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7985 (mmmt) REVERT: A 119 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8619 (ttmm) REVERT: A 178 ASP cc_start: 0.7994 (m-30) cc_final: 0.7214 (m-30) REVERT: A 214 GLN cc_start: 0.8048 (tt0) cc_final: 0.7327 (mm-40) REVERT: A 444 LYS cc_start: 0.8293 (mtpp) cc_final: 0.8058 (mtmt) REVERT: A 514 LYS cc_start: 0.7670 (ptpt) cc_final: 0.7142 (pttt) REVERT: A 518 GLU cc_start: 0.7893 (tt0) cc_final: 0.7531 (mt-10) REVERT: A 736 ARG cc_start: 0.8177 (mmt90) cc_final: 0.7451 (mmp80) REVERT: A 999 LYS cc_start: 0.8032 (tppt) cc_final: 0.7669 (mttm) REVERT: A 1015 MET cc_start: 0.8132 (mmm) cc_final: 0.7824 (mpp) REVERT: A 1271 TYR cc_start: 0.6297 (OUTLIER) cc_final: 0.5329 (t80) REVERT: A 1280 PHE cc_start: 0.7485 (m-10) cc_final: 0.7189 (m-10) REVERT: A 1375 ARG cc_start: 0.8445 (ttm110) cc_final: 0.7584 (ttt-90) REVERT: A 1383 SER cc_start: 0.8033 (m) cc_final: 0.7322 (p) REVERT: A 1384 ASN cc_start: 0.7890 (t0) cc_final: 0.7666 (m-40) REVERT: B 182 ARG cc_start: 0.7783 (tpp80) cc_final: 0.7068 (ttm-80) REVERT: B 188 ARG cc_start: 0.6232 (mmp80) cc_final: 0.5353 (tpt90) REVERT: B 202 ASN cc_start: 0.8918 (m110) cc_final: 0.8240 (m110) REVERT: C 177 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8295 (mm-30) outliers start: 30 outliers final: 20 residues processed: 209 average time/residue: 0.1280 time to fit residues: 37.4621 Evaluate side-chains 200 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1258 MET Chi-restraints excluded: chain A residue 1271 TYR Chi-restraints excluded: chain A residue 1311 ASP Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1362 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 67 optimal weight: 0.0370 chunk 100 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 150 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 ASN E 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.170227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134379 restraints weight = 37347.468| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 4.81 r_work: 0.3269 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13787 Z= 0.118 Angle : 0.543 7.074 18715 Z= 0.268 Chirality : 0.039 0.173 2109 Planarity : 0.004 0.044 2391 Dihedral : 4.238 24.647 1836 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.61 % Allowed : 13.99 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.99 (0.21), residues: 1680 helix: 1.23 (0.18), residues: 891 sheet: -0.93 (0.49), residues: 102 loop : 0.33 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.012 0.001 TYR A 153 PHE 0.017 0.001 PHE A 983 TRP 0.015 0.001 TRP A1019 HIS 0.004 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00276 (13782) covalent geometry : angle 0.54150 (18711) SS BOND : bond 0.00015 ( 1) SS BOND : angle 1.48260 ( 2) hydrogen bonds : bond 0.03416 ( 667) hydrogen bonds : angle 4.50190 ( 1903) metal coordination : bond 0.01233 ( 4) metal coordination : angle 2.99783 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8109 (tpm170) cc_final: 0.7821 (tpm170) REVERT: A 48 LYS cc_start: 0.8312 (mmmt) cc_final: 0.8035 (mmmt) REVERT: A 119 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8616 (ttmm) REVERT: A 178 ASP cc_start: 0.8078 (m-30) cc_final: 0.7307 (m-30) REVERT: A 214 GLN cc_start: 0.8083 (tt0) cc_final: 0.7365 (mm-40) REVERT: A 444 LYS cc_start: 0.8264 (mtpp) cc_final: 0.8006 (mtmt) REVERT: A 514 LYS cc_start: 0.7548 (ptpt) cc_final: 0.6997 (pttt) REVERT: A 518 GLU cc_start: 0.7913 (tt0) cc_final: 0.7474 (mt-10) REVERT: A 736 ARG cc_start: 0.8154 (mmt90) cc_final: 0.7326 (mmt90) REVERT: A 999 LYS cc_start: 0.8047 (tppt) cc_final: 0.7691 (mttm) REVERT: A 1015 MET cc_start: 0.8212 (mmm) cc_final: 0.7912 (mpp) REVERT: A 1217 ARG cc_start: 0.6957 (ttm110) cc_final: 0.6614 (ttp80) REVERT: A 1271 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.5222 (t80) REVERT: A 1280 PHE cc_start: 0.7352 (m-10) cc_final: 0.6903 (m-10) REVERT: A 1375 ARG cc_start: 0.8456 (ttm110) cc_final: 0.7613 (ttt-90) REVERT: A 1383 SER cc_start: 0.7961 (m) cc_final: 0.7446 (p) REVERT: B 148 THR cc_start: 0.7854 (p) cc_final: 0.7573 (p) REVERT: B 182 ARG cc_start: 0.7757 (tpp80) cc_final: 0.7101 (ttm-80) REVERT: B 188 ARG cc_start: 0.6308 (mmp80) cc_final: 0.5323 (tpt90) REVERT: B 202 ASN cc_start: 0.8714 (m110) cc_final: 0.8073 (m110) REVERT: C 177 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8321 (mm-30) REVERT: D 124 MET cc_start: 0.5413 (tpp) cc_final: 0.4988 (tpp) outliers start: 24 outliers final: 15 residues processed: 207 average time/residue: 0.1321 time to fit residues: 38.3901 Evaluate side-chains 200 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1271 TYR Chi-restraints excluded: chain A residue 1311 ASP Chi-restraints excluded: chain A residue 1326 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 151 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 144 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 154 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 ASN E 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.169273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.135871 restraints weight = 28626.770| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.88 r_work: 0.3424 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13787 Z= 0.111 Angle : 0.550 9.774 18715 Z= 0.269 Chirality : 0.040 0.185 2109 Planarity : 0.004 0.043 2391 Dihedral : 4.154 24.631 1836 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.74 % Allowed : 13.92 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.15 (0.21), residues: 1680 helix: 1.35 (0.18), residues: 892 sheet: -0.79 (0.50), residues: 102 loop : 0.40 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.012 0.001 TYR A 153 PHE 0.023 0.001 PHE A1011 TRP 0.015 0.001 TRP A1019 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00261 (13782) covalent geometry : angle 0.54924 (18711) SS BOND : bond 0.00052 ( 1) SS BOND : angle 1.31083 ( 2) hydrogen bonds : bond 0.03343 ( 667) hydrogen bonds : angle 4.42738 ( 1903) metal coordination : bond 0.01190 ( 4) metal coordination : angle 2.75885 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8267 (mmmt) cc_final: 0.8043 (mmmt) REVERT: A 119 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8626 (ttmm) REVERT: A 178 ASP cc_start: 0.7858 (m-30) cc_final: 0.7041 (m-30) REVERT: A 214 GLN cc_start: 0.7982 (tt0) cc_final: 0.7454 (mm110) REVERT: A 514 LYS cc_start: 0.7450 (ptpt) cc_final: 0.6993 (pttt) REVERT: A 518 GLU cc_start: 0.7814 (tt0) cc_final: 0.7511 (mt-10) REVERT: A 736 ARG cc_start: 0.8150 (mmt90) cc_final: 0.7446 (mmp80) REVERT: A 999 LYS cc_start: 0.8009 (tppt) cc_final: 0.7655 (mttm) REVERT: A 1015 MET cc_start: 0.8152 (mmm) cc_final: 0.7889 (mmm) REVERT: A 1217 ARG cc_start: 0.6949 (ttm110) cc_final: 0.6647 (ttp80) REVERT: A 1271 TYR cc_start: 0.6239 (OUTLIER) cc_final: 0.5368 (t80) REVERT: A 1375 ARG cc_start: 0.8427 (ttm110) cc_final: 0.7672 (ttt-90) REVERT: A 1383 SER cc_start: 0.7839 (m) cc_final: 0.7176 (p) REVERT: A 1384 ASN cc_start: 0.7863 (t0) cc_final: 0.7638 (m-40) REVERT: B 148 THR cc_start: 0.7778 (p) cc_final: 0.7534 (p) REVERT: B 182 ARG cc_start: 0.7804 (tpp80) cc_final: 0.7149 (ttm-80) REVERT: B 188 ARG cc_start: 0.6272 (mmp80) cc_final: 0.5302 (tpt90) REVERT: B 202 ASN cc_start: 0.8559 (m110) cc_final: 0.7930 (m110) REVERT: C 177 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8203 (mm-30) REVERT: E 124 MET cc_start: 0.6662 (ppp) cc_final: 0.6425 (ptt) outliers start: 26 outliers final: 16 residues processed: 212 average time/residue: 0.1354 time to fit residues: 40.6863 Evaluate side-chains 202 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1258 MET Chi-restraints excluded: chain A residue 1271 TYR Chi-restraints excluded: chain A residue 1311 ASP Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain B residue 124 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 118 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 ASN ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.171261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.135487 restraints weight = 26062.787| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.83 r_work: 0.3394 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13787 Z= 0.117 Angle : 0.571 14.732 18715 Z= 0.276 Chirality : 0.040 0.168 2109 Planarity : 0.004 0.042 2391 Dihedral : 4.136 24.586 1836 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.47 % Allowed : 14.99 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.10 (0.21), residues: 1680 helix: 1.30 (0.18), residues: 900 sheet: -0.79 (0.51), residues: 100 loop : 0.37 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.013 0.001 TYR A1381 PHE 0.016 0.001 PHE A 411 TRP 0.014 0.001 TRP A1019 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00279 (13782) covalent geometry : angle 0.56991 (18711) SS BOND : bond 0.00040 ( 1) SS BOND : angle 1.22334 ( 2) hydrogen bonds : bond 0.03324 ( 667) hydrogen bonds : angle 4.42302 ( 1903) metal coordination : bond 0.01084 ( 4) metal coordination : angle 2.67359 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8238 (mmmt) cc_final: 0.8009 (mmmt) REVERT: A 119 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8612 (ttmm) REVERT: A 178 ASP cc_start: 0.7903 (m-30) cc_final: 0.7091 (m-30) REVERT: A 214 GLN cc_start: 0.7966 (tt0) cc_final: 0.7397 (mm110) REVERT: A 514 LYS cc_start: 0.7458 (ptpt) cc_final: 0.6976 (pttt) REVERT: A 518 GLU cc_start: 0.7774 (tt0) cc_final: 0.7443 (mt-10) REVERT: A 635 LYS cc_start: 0.7941 (mmmm) cc_final: 0.7658 (mmtm) REVERT: A 941 ARG cc_start: 0.8390 (ttp80) cc_final: 0.8139 (ttp80) REVERT: A 968 ASN cc_start: 0.7551 (m-40) cc_final: 0.7344 (m-40) REVERT: A 999 LYS cc_start: 0.7983 (tppt) cc_final: 0.7637 (mttm) REVERT: A 1015 MET cc_start: 0.8103 (mmm) cc_final: 0.7873 (mmm) REVERT: A 1217 ARG cc_start: 0.6995 (ttm110) cc_final: 0.6653 (ttp80) REVERT: A 1271 TYR cc_start: 0.6249 (OUTLIER) cc_final: 0.5379 (t80) REVERT: A 1375 ARG cc_start: 0.8414 (ttm110) cc_final: 0.7645 (ttt-90) REVERT: A 1383 SER cc_start: 0.7825 (m) cc_final: 0.7144 (p) REVERT: A 1384 ASN cc_start: 0.7824 (t0) cc_final: 0.7582 (m-40) REVERT: B 148 THR cc_start: 0.7740 (p) cc_final: 0.7491 (p) REVERT: B 182 ARG cc_start: 0.7751 (tpp80) cc_final: 0.7006 (ttm-80) REVERT: B 188 ARG cc_start: 0.6301 (mmp80) cc_final: 0.5298 (tpt90) REVERT: B 202 ASN cc_start: 0.8536 (m110) cc_final: 0.7851 (m110) REVERT: B 204 ASN cc_start: 0.8201 (t0) cc_final: 0.7730 (m-40) REVERT: C 177 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8227 (mm-30) outliers start: 22 outliers final: 15 residues processed: 210 average time/residue: 0.1429 time to fit residues: 42.2954 Evaluate side-chains 200 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1271 TYR Chi-restraints excluded: chain A residue 1311 ASP Chi-restraints excluded: chain A residue 1326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 125 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 ASN E 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.170629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134753 restraints weight = 32349.908| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.84 r_work: 0.3331 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13787 Z= 0.133 Angle : 0.591 18.581 18715 Z= 0.282 Chirality : 0.040 0.194 2109 Planarity : 0.004 0.042 2391 Dihedral : 4.175 24.649 1836 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.41 % Allowed : 15.19 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.07 (0.21), residues: 1680 helix: 1.28 (0.18), residues: 900 sheet: -0.83 (0.51), residues: 100 loop : 0.35 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 197 TYR 0.017 0.001 TYR A1381 PHE 0.028 0.001 PHE A1011 TRP 0.015 0.001 TRP A1019 HIS 0.005 0.001 HIS A 864 Details of bonding type rmsd covalent geometry : bond 0.00324 (13782) covalent geometry : angle 0.58984 (18711) SS BOND : bond 0.00021 ( 1) SS BOND : angle 1.22801 ( 2) hydrogen bonds : bond 0.03396 ( 667) hydrogen bonds : angle 4.46880 ( 1903) metal coordination : bond 0.01005 ( 4) metal coordination : angle 2.77975 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8285 (mmmt) cc_final: 0.8026 (mmmt) REVERT: A 119 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8589 (ttmm) REVERT: A 178 ASP cc_start: 0.7997 (m-30) cc_final: 0.7205 (m-30) REVERT: A 214 GLN cc_start: 0.8013 (tt0) cc_final: 0.7371 (mm-40) REVERT: A 514 LYS cc_start: 0.7503 (ptpt) cc_final: 0.7009 (pttt) REVERT: A 518 GLU cc_start: 0.7866 (tt0) cc_final: 0.7496 (mt-10) REVERT: A 635 LYS cc_start: 0.8037 (mmmm) cc_final: 0.7652 (mmtm) REVERT: A 941 ARG cc_start: 0.8473 (ttp80) cc_final: 0.8217 (ttp80) REVERT: A 999 LYS cc_start: 0.7983 (tppt) cc_final: 0.7668 (mttm) REVERT: A 1015 MET cc_start: 0.8208 (mmm) cc_final: 0.7998 (mmm) REVERT: A 1217 ARG cc_start: 0.7054 (ttm110) cc_final: 0.6653 (ttp80) REVERT: A 1271 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.5440 (t80) REVERT: A 1375 ARG cc_start: 0.8434 (ttm110) cc_final: 0.7646 (ttt-90) REVERT: A 1383 SER cc_start: 0.7826 (m) cc_final: 0.7111 (p) REVERT: A 1384 ASN cc_start: 0.7831 (t0) cc_final: 0.7579 (m-40) REVERT: B 148 THR cc_start: 0.7852 (p) cc_final: 0.7604 (p) REVERT: B 182 ARG cc_start: 0.7776 (tpp80) cc_final: 0.7149 (ttm-80) REVERT: B 188 ARG cc_start: 0.6333 (mmp80) cc_final: 0.5296 (tpt90) REVERT: B 202 ASN cc_start: 0.8582 (m110) cc_final: 0.7890 (m110) outliers start: 21 outliers final: 15 residues processed: 201 average time/residue: 0.1422 time to fit residues: 39.9317 Evaluate side-chains 202 residues out of total 1492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1271 TYR Chi-restraints excluded: chain A residue 1311 ASP Chi-restraints excluded: chain A residue 1326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 152 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.171234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.135015 restraints weight = 30284.527| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.47 r_work: 0.3364 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13787 Z= 0.120 Angle : 0.577 17.102 18715 Z= 0.277 Chirality : 0.040 0.161 2109 Planarity : 0.004 0.041 2391 Dihedral : 4.140 24.681 1836 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.74 % Allowed : 14.93 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.14 (0.21), residues: 1680 helix: 1.33 (0.18), residues: 899 sheet: -0.83 (0.50), residues: 100 loop : 0.40 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 197 TYR 0.022 0.001 TYR A1381 PHE 0.017 0.001 PHE A 411 TRP 0.016 0.001 TRP A1019 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00289 (13782) covalent geometry : angle 0.57664 (18711) SS BOND : bond 0.00030 ( 1) SS BOND : angle 1.14026 ( 2) hydrogen bonds : bond 0.03273 ( 667) hydrogen bonds : angle 4.43079 ( 1903) metal coordination : bond 0.01111 ( 4) metal coordination : angle 2.75057 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3394.70 seconds wall clock time: 59 minutes 6.86 seconds (3546.86 seconds total)