Starting phenix.real_space_refine on Sat Aug 23 03:53:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wi4_37557/08_2025/8wi4_37557.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wi4_37557/08_2025/8wi4_37557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wi4_37557/08_2025/8wi4_37557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wi4_37557/08_2025/8wi4_37557.map" model { file = "/net/cci-nas-00/data/ceres_data/8wi4_37557/08_2025/8wi4_37557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wi4_37557/08_2025/8wi4_37557.cif" } resolution = 3.2 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= 0.070 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 6054 2.51 5 N 1616 2.21 5 O 1715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9443 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1207, 9443 Classifications: {'peptide': 1207} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 1171} Chain breaks: 3 Time building chain proxies: 2.33, per 1000 atoms: 0.25 Number of scatterers: 9443 At special positions: 0 Unit cell: (85.32, 110.16, 146.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1715 8.00 N 1616 7.00 C 6054 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 399.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 5 sheets defined 67.5% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 113 through 116 Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 141 through 160 removed outlier: 3.562A pdb=" N ASN A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 210 removed outlier: 3.508A pdb=" N VAL A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N THR A 177 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG A 178 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Proline residue: A 197 - end of helix removed outlier: 3.907A pdb=" N VAL A 201 " --> pdb=" O PRO A 197 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 264 removed outlier: 3.733A pdb=" N SER A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 removed outlier: 4.003A pdb=" N LYS A 271 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 282 removed outlier: 3.740A pdb=" N ILE A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 294 Processing helix chain 'A' and resid 295 through 298 removed outlier: 4.430A pdb=" N ALA A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 298' Processing helix chain 'A' and resid 299 through 310 Processing helix chain 'A' and resid 318 through 344 removed outlier: 3.903A pdb=" N GLY A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) Proline residue: A 331 - end of helix removed outlier: 4.338A pdb=" N PHE A 335 " --> pdb=" O PRO A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 364 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.569A pdb=" N ILE A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 400 removed outlier: 3.584A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 405 through 422 removed outlier: 4.009A pdb=" N VAL A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 444 removed outlier: 3.875A pdb=" N VAL A 436 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 472 Processing helix chain 'A' and resid 600 through 610 Processing helix chain 'A' and resid 640 through 645 removed outlier: 3.616A pdb=" N LEU A 644 " --> pdb=" O ARG A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 662 Processing helix chain 'A' and resid 663 through 670 Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 686 through 702 removed outlier: 3.818A pdb=" N ASP A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 728 Processing helix chain 'A' and resid 730 through 734 removed outlier: 3.574A pdb=" N LYS A 733 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER A 734 " --> pdb=" O HIS A 731 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 730 through 734' Processing helix chain 'A' and resid 766 through 773 Processing helix chain 'A' and resid 775 through 787 Processing helix chain 'A' and resid 842 through 854 removed outlier: 4.273A pdb=" N TYR A 846 " --> pdb=" O PRO A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 887 removed outlier: 3.903A pdb=" N THR A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 908 Processing helix chain 'A' and resid 910 through 958 removed outlier: 3.504A pdb=" N TYR A 914 " --> pdb=" O HIS A 910 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 937 " --> pdb=" O GLY A 933 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS A 938 " --> pdb=" O VAL A 934 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 943 " --> pdb=" O GLY A 939 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 944 " --> pdb=" O THR A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 966 removed outlier: 4.181A pdb=" N PHE A 963 " --> pdb=" O PRO A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 977 removed outlier: 3.824A pdb=" N ARG A 974 " --> pdb=" O ARG A 970 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE A 975 " --> pdb=" O ILE A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 985 Processing helix chain 'A' and resid 985 through 1011 removed outlier: 3.514A pdb=" N MET A 992 " --> pdb=" O ALA A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1032 removed outlier: 3.869A pdb=" N ALA A1017 " --> pdb=" O TRP A1013 " (cutoff:3.500A) Proline residue: A1020 - end of helix Processing helix chain 'A' and resid 1033 through 1052 Proline residue: A1049 - end of helix Processing helix chain 'A' and resid 1054 through 1060 Processing helix chain 'A' and resid 1061 through 1068 Processing helix chain 'A' and resid 1069 through 1120 removed outlier: 3.927A pdb=" N PHE A1073 " --> pdb=" O LYS A1069 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A1074 " --> pdb=" O GLY A1070 " (cutoff:3.500A) Proline residue: A1087 - end of helix removed outlier: 3.549A pdb=" N MET A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A1096 " --> pdb=" O THR A1092 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A1108 " --> pdb=" O LEU A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1139 Processing helix chain 'A' and resid 1142 through 1164 removed outlier: 3.806A pdb=" N THR A1158 " --> pdb=" O GLU A1154 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER A1159 " --> pdb=" O ALA A1155 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A1160 " --> pdb=" O ARG A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1242 Processing helix chain 'A' and resid 1262 through 1267 Processing helix chain 'A' and resid 1283 through 1289 Processing helix chain 'A' and resid 1295 through 1306 Processing helix chain 'A' and resid 1308 through 1314 removed outlier: 3.585A pdb=" N ILE A1312 " --> pdb=" O MET A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1328 Processing helix chain 'A' and resid 1331 through 1342 Processing helix chain 'A' and resid 1363 through 1376 Processing helix chain 'A' and resid 1410 through 1417 removed outlier: 3.523A pdb=" N ASN A1417 " --> pdb=" O VAL A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1432 removed outlier: 3.553A pdb=" N ALA A1424 " --> pdb=" O SER A1420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 584 through 586 removed outlier: 7.121A pdb=" N ILE A 585 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 625 through 628 removed outlier: 3.678A pdb=" N VAL A 591 " --> pdb=" O VAL A 737 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 754 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS A 594 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N PHE A 755 " --> pdb=" O THR A 762 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1210 through 1216 removed outlier: 7.407A pdb=" N LYS A1211 " --> pdb=" O GLU A1199 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLU A1199 " --> pdb=" O LYS A1211 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL A1213 " --> pdb=" O ASN A1197 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALA A1198 " --> pdb=" O GLY A1248 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY A1248 " --> pdb=" O ALA A1198 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1224 through 1225 Processing sheet with id=AA5, first strand: chain 'A' and resid 1398 through 1401 removed outlier: 6.736A pdb=" N VAL A1399 " --> pdb=" O VAL A1406 " (cutoff:3.500A) 559 hydrogen bonds defined for protein. 1644 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: 1.73 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2090 1.33 - 1.45: 2015 1.45 - 1.58: 5416 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 9619 Sorted by residual: bond pdb=" N VAL A1413 " pdb=" CA VAL A1413 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 8.03e+00 bond pdb=" N VAL A 848 " pdb=" CA VAL A 848 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.26e-02 6.30e+03 7.96e+00 bond pdb=" N THR A1410 " pdb=" CA THR A1410 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.41e-02 5.03e+03 7.33e+00 bond pdb=" N VAL A 845 " pdb=" CA VAL A 845 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.12e+00 bond pdb=" N SER A1412 " pdb=" CA SER A1412 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.16e-02 7.43e+03 6.23e+00 ... (remaining 9614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 12853 2.14 - 4.28: 136 4.28 - 6.42: 21 6.42 - 8.55: 6 8.55 - 10.69: 2 Bond angle restraints: 13018 Sorted by residual: angle pdb=" C SER A1032 " pdb=" N ARG A1033 " pdb=" CA ARG A1033 " ideal model delta sigma weight residual 121.54 128.85 -7.31 1.91e+00 2.74e-01 1.46e+01 angle pdb=" CB MET A1360 " pdb=" CG MET A1360 " pdb=" SD MET A1360 " ideal model delta sigma weight residual 112.70 123.39 -10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CA LEU A1415 " pdb=" C LEU A1415 " pdb=" O LEU A1415 " ideal model delta sigma weight residual 120.82 117.30 3.52 1.05e+00 9.07e-01 1.12e+01 angle pdb=" CA ASP A1409 " pdb=" C ASP A1409 " pdb=" O ASP A1409 " ideal model delta sigma weight residual 120.51 115.94 4.57 1.43e+00 4.89e-01 1.02e+01 angle pdb=" CA PHE A1408 " pdb=" C PHE A1408 " pdb=" N ASP A1409 " ideal model delta sigma weight residual 116.33 112.23 4.10 1.32e+00 5.74e-01 9.66e+00 ... (remaining 13013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 4793 17.25 - 34.49: 715 34.49 - 51.74: 230 51.74 - 68.99: 38 68.99 - 86.23: 13 Dihedral angle restraints: 5789 sinusoidal: 2288 harmonic: 3501 Sorted by residual: dihedral pdb=" CA PHE A 739 " pdb=" C PHE A 739 " pdb=" N VAL A 740 " pdb=" CA VAL A 740 " ideal model delta harmonic sigma weight residual -180.00 -161.93 -18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA LEU A1236 " pdb=" C LEU A1236 " pdb=" N GLY A1237 " pdb=" CA GLY A1237 " ideal model delta harmonic sigma weight residual -180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA TRP A 843 " pdb=" CB TRP A 843 " pdb=" CG TRP A 843 " pdb=" CD1 TRP A 843 " ideal model delta sinusoidal sigma weight residual 90.00 159.50 -69.50 2 2.00e+01 2.50e-03 1.05e+01 ... (remaining 5786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1129 0.037 - 0.075: 301 0.075 - 0.112: 83 0.112 - 0.149: 11 0.149 - 0.187: 4 Chirality restraints: 1528 Sorted by residual: chirality pdb=" CA LEU A1414 " pdb=" N LEU A1414 " pdb=" C LEU A1414 " pdb=" CB LEU A1414 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA VAL A 845 " pdb=" N VAL A 845 " pdb=" C VAL A 845 " pdb=" CB VAL A 845 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB ILE A1352 " pdb=" CA ILE A1352 " pdb=" CG1 ILE A1352 " pdb=" CG2 ILE A1352 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 1525 not shown) Planarity restraints: 1633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1408 " 0.021 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C PHE A1408 " -0.075 2.00e-02 2.50e+03 pdb=" O PHE A1408 " 0.029 2.00e-02 2.50e+03 pdb=" N ASP A1409 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 958 " 0.058 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO A 959 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 959 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 959 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1276 " 0.053 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO A1277 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A1277 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1277 " 0.043 5.00e-02 4.00e+02 ... (remaining 1630 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2392 2.80 - 3.33: 9301 3.33 - 3.85: 15795 3.85 - 4.38: 17244 4.38 - 4.90: 30474 Nonbonded interactions: 75206 Sorted by model distance: nonbonded pdb=" OG1 THR A 189 " pdb=" O ARG A 232 " model vdw 2.276 3.040 nonbonded pdb=" O ASN A 869 " pdb=" OG SER A 872 " model vdw 2.294 3.040 nonbonded pdb=" O SER A 596 " pdb=" OG SER A 599 " model vdw 2.317 3.040 nonbonded pdb=" O ILE A 955 " pdb=" OG SER A 958 " model vdw 2.321 3.040 nonbonded pdb=" OG SER A 142 " pdb=" OD1 ASP A1082 " model vdw 2.321 3.040 ... (remaining 75201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.930 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9619 Z= 0.144 Angle : 0.570 10.693 13018 Z= 0.325 Chirality : 0.038 0.187 1528 Planarity : 0.004 0.087 1633 Dihedral : 18.331 86.232 3521 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.17 % Favored : 94.33 % Rotamer: Outliers : 0.39 % Allowed : 31.75 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.03 (0.26), residues: 1199 helix: 1.72 (0.20), residues: 745 sheet: -1.80 (1.10), residues: 24 loop : -1.03 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1373 TYR 0.018 0.001 TYR A 700 PHE 0.020 0.001 PHE A 739 TRP 0.009 0.001 TRP A 843 HIS 0.006 0.000 HIS A 767 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9619) covalent geometry : angle 0.56982 (13018) hydrogen bonds : bond 0.14367 ( 559) hydrogen bonds : angle 5.51605 ( 1644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.352 Fit side-chains REVERT: A 1398 MET cc_start: 0.7573 (ptm) cc_final: 0.7310 (ptm) outliers start: 4 outliers final: 1 residues processed: 129 average time/residue: 0.0709 time to fit residues: 14.6911 Evaluate side-chains 118 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1413 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.1980 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 0.0980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 743 GLN ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.205631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.157436 restraints weight = 12267.835| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.43 r_work: 0.3759 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9619 Z= 0.111 Angle : 0.513 9.033 13018 Z= 0.266 Chirality : 0.038 0.150 1528 Planarity : 0.004 0.063 1633 Dihedral : 3.695 24.446 1301 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.34 % Favored : 94.25 % Rotamer: Outliers : 2.52 % Allowed : 29.91 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.26), residues: 1199 helix: 1.63 (0.20), residues: 760 sheet: -1.61 (1.09), residues: 24 loop : -1.05 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1101 TYR 0.008 0.001 TYR A1135 PHE 0.015 0.001 PHE A 335 TRP 0.014 0.001 TRP A1097 HIS 0.004 0.001 HIS A 767 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9619) covalent geometry : angle 0.51303 (13018) hydrogen bonds : bond 0.03414 ( 559) hydrogen bonds : angle 4.27899 ( 1644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 970 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7680 (ttt180) REVERT: A 1058 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7922 (mp) REVERT: A 1131 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7024 (pp) REVERT: A 1309 LYS cc_start: 0.8187 (tppp) cc_final: 0.7932 (ttpp) REVERT: A 1317 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6495 (tt) outliers start: 26 outliers final: 12 residues processed: 139 average time/residue: 0.0818 time to fit residues: 17.3094 Evaluate side-chains 132 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 767 HIS Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1413 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 98 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1197 ASN ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.189941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142714 restraints weight = 12074.466| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.31 r_work: 0.3499 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9619 Z= 0.200 Angle : 0.591 9.385 13018 Z= 0.311 Chirality : 0.041 0.143 1528 Planarity : 0.005 0.059 1633 Dihedral : 4.023 23.053 1301 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.00 % Favored : 94.58 % Rotamer: Outliers : 3.29 % Allowed : 28.75 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.60 (0.25), residues: 1199 helix: 1.24 (0.19), residues: 762 sheet: -1.12 (1.13), residues: 24 loop : -1.06 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1335 TYR 0.018 0.001 TYR A1135 PHE 0.017 0.002 PHE A1014 TRP 0.014 0.002 TRP A1097 HIS 0.005 0.001 HIS A1121 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9619) covalent geometry : angle 0.59149 (13018) hydrogen bonds : bond 0.04603 ( 559) hydrogen bonds : angle 4.52648 ( 1644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 109 CYS cc_start: 0.9047 (t) cc_final: 0.8270 (m) REVERT: A 330 TYR cc_start: 0.5000 (t80) cc_final: 0.2154 (t80) REVERT: A 333 MET cc_start: 0.8550 (mmp) cc_final: 0.8240 (mmp) REVERT: A 408 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8460 (mp) REVERT: A 491 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7957 (tm-30) REVERT: A 771 MET cc_start: 0.7901 (mmm) cc_final: 0.7654 (mmm) REVERT: A 953 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8346 (ttp80) REVERT: A 1058 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8505 (mt) REVERT: A 1252 LYS cc_start: 0.8472 (mttt) cc_final: 0.8116 (mttt) REVERT: A 1309 LYS cc_start: 0.8500 (tppp) cc_final: 0.7819 (ttpp) REVERT: A 1373 ARG cc_start: 0.8640 (mtm-85) cc_final: 0.8400 (mtm-85) outliers start: 34 outliers final: 15 residues processed: 153 average time/residue: 0.0937 time to fit residues: 20.4027 Evaluate side-chains 139 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 0 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 chunk 7 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 722 HIS A 869 ASN ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.188835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140275 restraints weight = 11944.945| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.05 r_work: 0.3515 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9619 Z= 0.119 Angle : 0.520 9.338 13018 Z= 0.273 Chirality : 0.038 0.137 1528 Planarity : 0.004 0.056 1633 Dihedral : 3.923 23.943 1300 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.84 % Favored : 94.75 % Rotamer: Outliers : 3.68 % Allowed : 27.98 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.25), residues: 1199 helix: 1.37 (0.19), residues: 761 sheet: -1.06 (1.13), residues: 24 loop : -1.08 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 345 TYR 0.012 0.001 TYR A1135 PHE 0.021 0.001 PHE A 739 TRP 0.014 0.001 TRP A1097 HIS 0.009 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9619) covalent geometry : angle 0.52023 (13018) hydrogen bonds : bond 0.03855 ( 559) hydrogen bonds : angle 4.34024 ( 1644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 109 CYS cc_start: 0.8913 (t) cc_final: 0.8086 (m) REVERT: A 229 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: A 330 TYR cc_start: 0.4970 (t80) cc_final: 0.2137 (t80) REVERT: A 333 MET cc_start: 0.8583 (mmp) cc_final: 0.8319 (mmp) REVERT: A 408 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8394 (mp) REVERT: A 491 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7881 (tm-30) REVERT: A 771 MET cc_start: 0.7929 (mmm) cc_final: 0.7721 (mmm) REVERT: A 953 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8347 (ttp80) REVERT: A 970 ARG cc_start: 0.7664 (ttm170) cc_final: 0.7459 (ttp80) REVERT: A 1058 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8391 (mt) REVERT: A 1309 LYS cc_start: 0.8464 (tppp) cc_final: 0.8234 (ttpp) REVERT: A 1373 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.8095 (mtm-85) outliers start: 38 outliers final: 21 residues processed: 153 average time/residue: 0.0867 time to fit residues: 19.6492 Evaluate side-chains 144 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 722 HIS Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 87 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 0.0170 chunk 48 optimal weight: 0.7980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 722 HIS A 869 ASN ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.188335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139652 restraints weight = 11952.345| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.08 r_work: 0.3505 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9619 Z= 0.126 Angle : 0.525 9.027 13018 Z= 0.273 Chirality : 0.038 0.142 1528 Planarity : 0.004 0.054 1633 Dihedral : 3.904 24.144 1300 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.00 % Favored : 94.58 % Rotamer: Outliers : 3.10 % Allowed : 28.56 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.75 (0.25), residues: 1199 helix: 1.38 (0.19), residues: 761 sheet: -0.81 (1.20), residues: 24 loop : -1.08 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1346 TYR 0.016 0.001 TYR A1135 PHE 0.025 0.001 PHE A 739 TRP 0.013 0.001 TRP A1097 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9619) covalent geometry : angle 0.52510 (13018) hydrogen bonds : bond 0.03891 ( 559) hydrogen bonds : angle 4.33326 ( 1644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 109 CYS cc_start: 0.9028 (t) cc_final: 0.8194 (m) REVERT: A 229 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: A 330 TYR cc_start: 0.5059 (t80) cc_final: 0.2119 (t80) REVERT: A 333 MET cc_start: 0.8605 (mmp) cc_final: 0.8339 (mmp) REVERT: A 408 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8414 (mp) REVERT: A 491 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7812 (tm-30) REVERT: A 641 ASP cc_start: 0.7640 (m-30) cc_final: 0.7426 (p0) REVERT: A 771 MET cc_start: 0.7936 (mmm) cc_final: 0.7723 (mmm) REVERT: A 843 TRP cc_start: 0.7449 (m100) cc_final: 0.5384 (t-100) REVERT: A 970 ARG cc_start: 0.7656 (ttm170) cc_final: 0.7452 (ttp80) REVERT: A 1058 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8398 (mt) REVERT: A 1309 LYS cc_start: 0.8490 (tppp) cc_final: 0.8268 (ttpp) REVERT: A 1373 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.8032 (mtm-85) outliers start: 32 outliers final: 23 residues processed: 146 average time/residue: 0.0850 time to fit residues: 18.1195 Evaluate side-chains 144 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 722 HIS Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1033 ARG Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 98 optimal weight: 0.0570 chunk 38 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 HIS ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.187824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.139997 restraints weight = 11941.177| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.23 r_work: 0.3483 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9619 Z= 0.126 Angle : 0.531 9.048 13018 Z= 0.276 Chirality : 0.038 0.143 1528 Planarity : 0.004 0.052 1633 Dihedral : 3.928 24.790 1300 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.09 % Favored : 94.50 % Rotamer: Outliers : 3.87 % Allowed : 28.36 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.25), residues: 1199 helix: 1.39 (0.19), residues: 762 sheet: -0.76 (1.22), residues: 24 loop : -1.04 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1101 TYR 0.030 0.001 TYR A1135 PHE 0.026 0.001 PHE A 739 TRP 0.013 0.001 TRP A1097 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9619) covalent geometry : angle 0.53077 (13018) hydrogen bonds : bond 0.03850 ( 559) hydrogen bonds : angle 4.33211 ( 1644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 109 CYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8261 (m) REVERT: A 156 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: A 229 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: A 330 TYR cc_start: 0.5089 (t80) cc_final: 0.2096 (t80) REVERT: A 333 MET cc_start: 0.8612 (mmp) cc_final: 0.8335 (mmp) REVERT: A 408 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8389 (mp) REVERT: A 491 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7800 (tm-30) REVERT: A 641 ASP cc_start: 0.7831 (m-30) cc_final: 0.7533 (p0) REVERT: A 843 TRP cc_start: 0.7442 (m100) cc_final: 0.5322 (t-100) REVERT: A 953 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8489 (ttp80) REVERT: A 970 ARG cc_start: 0.7711 (ttm170) cc_final: 0.7458 (ttp80) REVERT: A 1058 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8406 (mt) REVERT: A 1308 MET cc_start: 0.4850 (tpt) cc_final: 0.4465 (tpt) REVERT: A 1309 LYS cc_start: 0.8561 (tppp) cc_final: 0.8313 (ttpp) REVERT: A 1373 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.8125 (mtm-85) outliers start: 40 outliers final: 25 residues processed: 149 average time/residue: 0.0800 time to fit residues: 17.5567 Evaluate side-chains 151 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 722 HIS Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1033 ARG Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 119 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 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 722 HIS ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.186908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.137541 restraints weight = 11899.930| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.06 r_work: 0.3461 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9619 Z= 0.133 Angle : 0.534 9.000 13018 Z= 0.278 Chirality : 0.039 0.155 1528 Planarity : 0.004 0.050 1633 Dihedral : 3.955 25.451 1300 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.00 % Favored : 94.58 % Rotamer: Outliers : 4.07 % Allowed : 27.49 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.75 (0.25), residues: 1199 helix: 1.37 (0.19), residues: 761 sheet: -0.65 (1.24), residues: 24 loop : -1.06 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1346 TYR 0.016 0.001 TYR A1135 PHE 0.027 0.001 PHE A 739 TRP 0.013 0.001 TRP A1097 HIS 0.015 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9619) covalent geometry : angle 0.53354 (13018) hydrogen bonds : bond 0.03918 ( 559) hydrogen bonds : angle 4.34871 ( 1644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.368 Fit side-chains REVERT: A 109 CYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8390 (m) REVERT: A 138 LYS cc_start: 0.8639 (pttp) cc_final: 0.8425 (pttp) REVERT: A 156 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: A 229 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: A 330 TYR cc_start: 0.5210 (t80) cc_final: 0.2136 (t80) REVERT: A 333 MET cc_start: 0.8636 (mmp) cc_final: 0.8342 (mmp) REVERT: A 408 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8367 (mp) REVERT: A 438 THR cc_start: 0.8849 (p) cc_final: 0.8581 (p) REVERT: A 491 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7807 (tm-30) REVERT: A 641 ASP cc_start: 0.7769 (m-30) cc_final: 0.7514 (p0) REVERT: A 843 TRP cc_start: 0.7483 (m100) cc_final: 0.5347 (t-100) REVERT: A 953 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8502 (ttp80) REVERT: A 1058 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8448 (mt) REVERT: A 1147 VAL cc_start: 0.8620 (t) cc_final: 0.8357 (m) REVERT: A 1308 MET cc_start: 0.4686 (tpt) cc_final: 0.4331 (tpt) REVERT: A 1373 ARG cc_start: 0.8450 (mtm-85) cc_final: 0.8102 (mtm-85) outliers start: 42 outliers final: 25 residues processed: 153 average time/residue: 0.0941 time to fit residues: 20.7753 Evaluate side-chains 151 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 767 HIS Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1033 ARG Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 49 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 113 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 95 optimal weight: 0.0870 chunk 54 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.186820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.137811 restraints weight = 11901.190| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.95 r_work: 0.3479 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9619 Z= 0.127 Angle : 0.531 8.986 13018 Z= 0.277 Chirality : 0.039 0.169 1528 Planarity : 0.004 0.049 1633 Dihedral : 3.985 25.704 1300 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.09 % Favored : 94.50 % Rotamer: Outliers : 3.10 % Allowed : 27.69 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.78 (0.25), residues: 1199 helix: 1.40 (0.19), residues: 760 sheet: -0.46 (1.27), residues: 24 loop : -1.05 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1346 TYR 0.015 0.001 TYR A1135 PHE 0.026 0.001 PHE A 739 TRP 0.014 0.001 TRP A1097 HIS 0.003 0.001 HIS A1307 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9619) covalent geometry : angle 0.53097 (13018) hydrogen bonds : bond 0.03865 ( 559) hydrogen bonds : angle 4.34748 ( 1644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.348 Fit side-chains REVERT: A 109 CYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8340 (m) REVERT: A 138 LYS cc_start: 0.8629 (pttp) cc_final: 0.8426 (pttp) REVERT: A 156 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: A 229 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: A 330 TYR cc_start: 0.5297 (t80) cc_final: 0.2166 (t80) REVERT: A 333 MET cc_start: 0.8662 (mmp) cc_final: 0.8341 (mmp) REVERT: A 408 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8362 (mp) REVERT: A 491 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7784 (tm-30) REVERT: A 641 ASP cc_start: 0.7676 (m-30) cc_final: 0.7460 (p0) REVERT: A 771 MET cc_start: 0.7689 (mmm) cc_final: 0.7480 (mmm) REVERT: A 843 TRP cc_start: 0.7532 (m100) cc_final: 0.5288 (t-100) REVERT: A 953 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8449 (ttp80) REVERT: A 1021 LEU cc_start: 0.8518 (mt) cc_final: 0.8163 (mt) REVERT: A 1058 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8464 (mt) REVERT: A 1147 VAL cc_start: 0.8624 (t) cc_final: 0.8384 (m) REVERT: A 1373 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8062 (mtm-85) outliers start: 32 outliers final: 23 residues processed: 145 average time/residue: 0.0975 time to fit residues: 20.4407 Evaluate side-chains 148 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 89 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 112 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.186229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.136624 restraints weight = 11793.416| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.98 r_work: 0.3469 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9619 Z= 0.132 Angle : 0.543 9.787 13018 Z= 0.281 Chirality : 0.039 0.161 1528 Planarity : 0.004 0.049 1633 Dihedral : 4.022 26.147 1300 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.09 % Favored : 94.50 % Rotamer: Outliers : 3.19 % Allowed : 27.59 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.25), residues: 1199 helix: 1.37 (0.19), residues: 760 sheet: -0.64 (1.25), residues: 24 loop : -1.04 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 985 TYR 0.016 0.001 TYR A1135 PHE 0.025 0.001 PHE A 739 TRP 0.014 0.001 TRP A1097 HIS 0.004 0.001 HIS A1307 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9619) covalent geometry : angle 0.54270 (13018) hydrogen bonds : bond 0.03917 ( 559) hydrogen bonds : angle 4.35178 ( 1644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.372 Fit side-chains REVERT: A 109 CYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8403 (m) REVERT: A 138 LYS cc_start: 0.8637 (pttp) cc_final: 0.8431 (pttp) REVERT: A 156 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: A 229 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: A 330 TYR cc_start: 0.5320 (t80) cc_final: 0.2240 (t80) REVERT: A 333 MET cc_start: 0.8614 (mmp) cc_final: 0.8270 (mmp) REVERT: A 408 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8412 (mp) REVERT: A 438 THR cc_start: 0.8865 (p) cc_final: 0.8605 (p) REVERT: A 491 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7776 (tm-30) REVERT: A 843 TRP cc_start: 0.7545 (m100) cc_final: 0.5329 (t-100) REVERT: A 953 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8455 (ttp80) REVERT: A 1021 LEU cc_start: 0.8547 (mt) cc_final: 0.8188 (mt) REVERT: A 1058 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8490 (mt) REVERT: A 1147 VAL cc_start: 0.8675 (t) cc_final: 0.8441 (m) REVERT: A 1309 LYS cc_start: 0.8542 (ttpp) cc_final: 0.8187 (ttpp) REVERT: A 1373 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.8070 (mtm-85) outliers start: 33 outliers final: 25 residues processed: 145 average time/residue: 0.0962 time to fit residues: 20.2049 Evaluate side-chains 149 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 767 HIS Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1033 ARG Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 0.5980 chunk 84 optimal weight: 0.0570 chunk 8 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.0370 chunk 32 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.188124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138925 restraints weight = 11869.363| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.91 r_work: 0.3493 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9619 Z= 0.111 Angle : 0.535 10.494 13018 Z= 0.274 Chirality : 0.038 0.161 1528 Planarity : 0.004 0.048 1633 Dihedral : 3.988 24.942 1300 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.59 % Favored : 95.00 % Rotamer: Outliers : 2.71 % Allowed : 28.65 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.25), residues: 1199 helix: 1.43 (0.19), residues: 760 sheet: -0.79 (1.23), residues: 24 loop : -1.03 (0.33), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 985 TYR 0.013 0.001 TYR A1135 PHE 0.029 0.001 PHE A 739 TRP 0.014 0.001 TRP A1097 HIS 0.004 0.001 HIS A 767 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9619) covalent geometry : angle 0.53527 (13018) hydrogen bonds : bond 0.03637 ( 559) hydrogen bonds : angle 4.28462 ( 1644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.360 Fit side-chains REVERT: A 109 CYS cc_start: 0.9196 (t) cc_final: 0.8400 (m) REVERT: A 156 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: A 229 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: A 330 TYR cc_start: 0.5151 (t80) cc_final: 0.2295 (t80) REVERT: A 333 MET cc_start: 0.8591 (mmp) cc_final: 0.8293 (mmp) REVERT: A 408 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8383 (mp) REVERT: A 491 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7732 (tm-30) REVERT: A 641 ASP cc_start: 0.7068 (p0) cc_final: 0.6637 (m-30) REVERT: A 843 TRP cc_start: 0.7480 (m100) cc_final: 0.5286 (t-100) REVERT: A 953 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8412 (mtm110) REVERT: A 1021 LEU cc_start: 0.8536 (mt) cc_final: 0.8180 (mt) REVERT: A 1058 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8423 (mt) REVERT: A 1147 VAL cc_start: 0.8611 (t) cc_final: 0.8377 (m) REVERT: A 1268 SER cc_start: 0.8788 (t) cc_final: 0.8460 (p) REVERT: A 1309 LYS cc_start: 0.8630 (ttpp) cc_final: 0.8282 (ttpp) REVERT: A 1373 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.8115 (mtm-85) outliers start: 28 outliers final: 20 residues processed: 140 average time/residue: 0.0899 time to fit residues: 18.5856 Evaluate side-chains 138 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 767 HIS Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 0.0870 chunk 108 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 869 ASN ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.185149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135414 restraints weight = 11787.781| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.00 r_work: 0.3449 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9619 Z= 0.146 Angle : 0.570 11.493 13018 Z= 0.293 Chirality : 0.039 0.148 1528 Planarity : 0.004 0.049 1633 Dihedral : 4.064 26.991 1300 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.50 % Favored : 94.08 % Rotamer: Outliers : 3.10 % Allowed : 28.07 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.66 (0.25), residues: 1199 helix: 1.24 (0.19), residues: 769 sheet: -0.88 (1.22), residues: 24 loop : -0.97 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1346 TYR 0.018 0.001 TYR A1135 PHE 0.030 0.001 PHE A 739 TRP 0.014 0.001 TRP A1097 HIS 0.005 0.001 HIS A 767 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9619) covalent geometry : angle 0.57024 (13018) hydrogen bonds : bond 0.04070 ( 559) hydrogen bonds : angle 4.38218 ( 1644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2729.54 seconds wall clock time: 47 minutes 31.03 seconds (2851.03 seconds total)