Starting phenix.real_space_refine on Tue May 13 01:09:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wi4_37557/05_2025/8wi4_37557.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wi4_37557/05_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_37557/05_2025/8wi4_37557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wi4_37557/05_2025/8wi4_37557.map" model { file = "/net/cci-nas-00/data/ceres_data/8wi4_37557/05_2025/8wi4_37557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wi4_37557/05_2025/8wi4_37557.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.80, per 1000 atoms: 0.61 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: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.98 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: 3.17 Time building geometry restraints manager: 2.64 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: 1.690 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.640 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.810 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP A 843 HIS 0.006 0.000 HIS A 767 PHE 0.020 0.001 PHE A 739 TYR 0.018 0.001 TYR A 700 ARG 0.002 0.000 ARG A1373 Details of bonding type rmsd hydrogen bonds : bond 0.14367 ( 559) hydrogen bonds : angle 5.51605 ( 1644) covalent geometry : bond 0.00253 ( 9619) covalent geometry : angle 0.56982 (13018) *********************** 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 : 1.066 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: 0.1594 time to fit residues: 32.6635 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 : 1.088 ------------------------------------------------------------------------------- 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 101 optimal weight: 0.0770 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.0870 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 = 0.4362 r_free = 0.4362 target = 0.202945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.153402 restraints weight = 12118.118| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.29 r_work: 0.3701 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9619 Z= 0.118 Angle : 0.525 8.972 13018 Z= 0.272 Chirality : 0.039 0.171 1528 Planarity : 0.004 0.064 1633 Dihedral : 3.748 24.521 1301 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.25 % Favored : 94.33 % Rotamer: Outliers : 2.71 % Allowed : 29.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1199 helix: 1.55 (0.20), residues: 762 sheet: -1.64 (1.08), residues: 24 loop : -1.03 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1097 HIS 0.005 0.001 HIS A 767 PHE 0.015 0.001 PHE A 335 TYR 0.009 0.001 TYR A1135 ARG 0.005 0.000 ARG A1101 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 559) hydrogen bonds : angle 4.29610 ( 1644) covalent geometry : bond 0.00248 ( 9619) covalent geometry : angle 0.52475 (13018) *********************** 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 152 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 739 PHE cc_start: 0.8179 (t80) cc_final: 0.7975 (t80) REVERT: A 1058 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.7968 (mp) REVERT: A 1131 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7043 (pp) REVERT: A 1309 LYS cc_start: 0.8153 (tppp) cc_final: 0.7916 (ttpp) REVERT: A 1317 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6555 (tt) outliers start: 28 outliers final: 13 residues processed: 144 average time/residue: 0.1806 time to fit residues: 38.6280 Evaluate side-chains 131 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 596 SER 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 60 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4195 r_free = 0.4195 target = 0.185800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.137999 restraints weight = 11923.106| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.42 r_work: 0.3454 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9619 Z= 0.189 Angle : 0.601 9.688 13018 Z= 0.316 Chirality : 0.041 0.146 1528 Planarity : 0.005 0.058 1633 Dihedral : 4.092 24.281 1301 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.84 % Favored : 94.75 % Rotamer: Outliers : 3.78 % Allowed : 28.17 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1199 helix: 1.19 (0.19), residues: 762 sheet: -1.04 (1.12), residues: 24 loop : -1.04 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1097 HIS 0.005 0.001 HIS A 421 PHE 0.018 0.002 PHE A1195 TYR 0.019 0.002 TYR A1135 ARG 0.004 0.000 ARG A1346 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 559) hydrogen bonds : angle 4.55123 ( 1644) covalent geometry : bond 0.00438 ( 9619) covalent geometry : angle 0.60101 (13018) *********************** 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 174 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 109 CYS cc_start: 0.9034 (t) cc_final: 0.8258 (m) REVERT: A 138 LYS cc_start: 0.8620 (pttp) cc_final: 0.8404 (pttp) REVERT: A 330 TYR cc_start: 0.5248 (t80) cc_final: 0.2249 (t80) REVERT: A 333 MET cc_start: 0.8532 (mmp) cc_final: 0.8141 (mmp) REVERT: A 408 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8429 (mp) REVERT: A 608 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7899 (tp) REVERT: A 953 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8274 (ttp80) REVERT: A 1058 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8561 (mt) REVERT: A 1252 LYS cc_start: 0.8516 (mttt) cc_final: 0.8128 (mttt) REVERT: A 1268 SER cc_start: 0.8750 (t) cc_final: 0.8419 (p) REVERT: A 1309 LYS cc_start: 0.8442 (tppp) cc_final: 0.7732 (ttpp) REVERT: A 1373 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.8320 (mtm-85) outliers start: 39 outliers final: 16 residues processed: 164 average time/residue: 0.2131 time to fit residues: 49.5278 Evaluate side-chains 143 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 429 THR 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 608 ILE 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 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 81 optimal weight: 0.2980 chunk 110 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 116 optimal weight: 0.1980 chunk 6 optimal weight: 0.0060 chunk 76 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 84 optimal weight: 0.6980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.188936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.139951 restraints weight = 11893.133| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.02 r_work: 0.3501 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9619 Z= 0.111 Angle : 0.515 9.274 13018 Z= 0.271 Chirality : 0.038 0.136 1528 Planarity : 0.004 0.056 1633 Dihedral : 3.927 24.155 1300 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.09 % Favored : 94.50 % Rotamer: Outliers : 3.48 % Allowed : 27.98 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1199 helix: 1.37 (0.19), residues: 761 sheet: -0.95 (1.14), residues: 24 loop : -1.06 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1097 HIS 0.008 0.001 HIS A 722 PHE 0.011 0.001 PHE A1157 TYR 0.008 0.001 TYR A1135 ARG 0.002 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 559) hydrogen bonds : angle 4.33388 ( 1644) covalent geometry : bond 0.00230 ( 9619) covalent geometry : angle 0.51468 (13018) *********************** 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 158 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 109 CYS cc_start: 0.8934 (t) cc_final: 0.8117 (m) REVERT: A 229 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: A 330 TYR cc_start: 0.4800 (t80) cc_final: 0.2043 (t80) REVERT: A 333 MET cc_start: 0.8489 (mmp) cc_final: 0.8123 (mmp) REVERT: A 408 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8343 (mp) REVERT: A 641 ASP cc_start: 0.7794 (m-30) cc_final: 0.7474 (p0) REVERT: A 771 MET cc_start: 0.8022 (mmm) cc_final: 0.7677 (mmm) REVERT: A 953 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8373 (ttp80) REVERT: A 1058 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8419 (mt) REVERT: A 1147 VAL cc_start: 0.8586 (t) cc_final: 0.8344 (m) REVERT: A 1309 LYS cc_start: 0.8536 (tppp) cc_final: 0.8273 (ttpp) REVERT: A 1324 MET cc_start: 0.7972 (mmt) cc_final: 0.7703 (mmt) outliers start: 36 outliers final: 20 residues processed: 149 average time/residue: 0.1839 time to fit residues: 40.2387 Evaluate side-chains 142 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 722 HIS Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 767 HIS Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 953 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 113 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 HIS A 869 ASN ** 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 = 0.4207 r_free = 0.4207 target = 0.187194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137821 restraints weight = 11818.457| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.96 r_work: 0.3490 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2951 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= 0.132 Angle : 0.527 9.012 13018 Z= 0.275 Chirality : 0.038 0.144 1528 Planarity : 0.004 0.054 1633 Dihedral : 3.928 24.762 1300 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.92 % Favored : 94.66 % Rotamer: Outliers : 3.58 % Allowed : 28.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1199 helix: 1.36 (0.19), residues: 760 sheet: -0.81 (1.18), residues: 24 loop : -1.08 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1097 HIS 0.015 0.001 HIS A 722 PHE 0.025 0.001 PHE A 739 TYR 0.012 0.001 TYR A1135 ARG 0.002 0.000 ARG A1346 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 559) hydrogen bonds : angle 4.33481 ( 1644) covalent geometry : bond 0.00294 ( 9619) covalent geometry : angle 0.52703 (13018) *********************** 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 155 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 109 CYS cc_start: 0.9032 (t) cc_final: 0.8215 (m) REVERT: A 156 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: A 229 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: A 330 TYR cc_start: 0.5105 (t80) cc_final: 0.2130 (t80) REVERT: A 333 MET cc_start: 0.8544 (mmp) cc_final: 0.8174 (mmp) REVERT: A 408 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8401 (mp) REVERT: A 438 THR cc_start: 0.8834 (p) cc_final: 0.8574 (p) REVERT: A 641 ASP cc_start: 0.7682 (m-30) cc_final: 0.7474 (p0) REVERT: A 771 MET cc_start: 0.7911 (mmm) cc_final: 0.7584 (mmm) REVERT: A 843 TRP cc_start: 0.7495 (m100) cc_final: 0.5478 (t-100) REVERT: A 953 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8445 (ttp80) REVERT: A 1058 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8423 (mt) REVERT: A 1147 VAL cc_start: 0.8629 (t) cc_final: 0.8398 (m) REVERT: A 1309 LYS cc_start: 0.8472 (tppp) cc_final: 0.8265 (ttpp) outliers start: 37 outliers final: 22 residues processed: 146 average time/residue: 0.1933 time to fit residues: 40.9138 Evaluate side-chains 141 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 248 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 314 ILE 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 590 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 857 LEU 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 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 98 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 2 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: ** 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 = 0.4204 r_free = 0.4204 target = 0.186894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137279 restraints weight = 11774.285| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.99 r_work: 0.3469 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9619 Z= 0.127 Angle : 0.529 9.110 13018 Z= 0.275 Chirality : 0.038 0.146 1528 Planarity : 0.004 0.052 1633 Dihedral : 3.965 25.745 1300 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.34 % Favored : 94.25 % Rotamer: Outliers : 3.48 % Allowed : 27.98 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1199 helix: 1.37 (0.19), residues: 760 sheet: -0.65 (1.22), residues: 24 loop : -1.06 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1097 HIS 0.004 0.001 HIS A 421 PHE 0.025 0.001 PHE A 739 TYR 0.011 0.001 TYR A1135 ARG 0.002 0.000 ARG A1346 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 559) hydrogen bonds : angle 4.32643 ( 1644) covalent geometry : bond 0.00281 ( 9619) covalent geometry : angle 0.52929 (13018) *********************** 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 157 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 1.090 Fit side-chains REVERT: A 109 CYS cc_start: 0.9111 (t) cc_final: 0.8306 (m) REVERT: A 138 LYS cc_start: 0.8625 (pttp) cc_final: 0.8409 (pttp) REVERT: A 156 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: A 229 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: A 330 TYR cc_start: 0.5043 (t80) cc_final: 0.2197 (t80) REVERT: A 333 MET cc_start: 0.8549 (mmp) cc_final: 0.8150 (mmp) REVERT: A 408 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8376 (mp) REVERT: A 438 THR cc_start: 0.8834 (p) cc_final: 0.8580 (p) REVERT: A 491 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7875 (tm-30) REVERT: A 641 ASP cc_start: 0.7797 (m-30) cc_final: 0.7527 (p0) REVERT: A 843 TRP cc_start: 0.7499 (m100) cc_final: 0.5382 (t-100) REVERT: A 953 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8447 (ttp80) REVERT: A 1058 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8436 (mt) REVERT: A 1147 VAL cc_start: 0.8621 (t) cc_final: 0.8375 (m) REVERT: A 1308 MET cc_start: 0.4601 (tpt) cc_final: 0.4232 (tpt) outliers start: 36 outliers final: 22 residues processed: 149 average time/residue: 0.2026 time to fit residues: 43.2675 Evaluate side-chains 144 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** 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 = 0.4154 r_free = 0.4154 target = 0.181920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.132996 restraints weight = 11870.581| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.20 r_work: 0.3399 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9619 Z= 0.199 Angle : 0.603 9.277 13018 Z= 0.315 Chirality : 0.041 0.155 1528 Planarity : 0.004 0.051 1633 Dihedral : 4.227 29.943 1300 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.25 % Favored : 94.33 % Rotamer: Outliers : 3.48 % Allowed : 27.20 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1199 helix: 1.07 (0.19), residues: 767 sheet: -0.64 (1.24), residues: 24 loop : -1.07 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 633 HIS 0.004 0.001 HIS A1121 PHE 0.024 0.002 PHE A 739 TYR 0.019 0.001 TYR A1135 ARG 0.004 0.000 ARG A1346 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 559) hydrogen bonds : angle 4.57028 ( 1644) covalent geometry : bond 0.00469 ( 9619) covalent geometry : angle 0.60341 (13018) *********************** 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 152 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 1.136 Fit side-chains REVERT: A 109 CYS cc_start: 0.9199 (t) cc_final: 0.8440 (m) REVERT: A 138 LYS cc_start: 0.8682 (pttp) cc_final: 0.8432 (pttp) REVERT: A 156 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: A 229 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: A 330 TYR cc_start: 0.5405 (t80) cc_final: 0.2439 (t80) REVERT: A 333 MET cc_start: 0.8620 (mmp) cc_final: 0.8127 (mmp) REVERT: A 408 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8425 (mp) REVERT: A 491 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 608 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7818 (tp) REVERT: A 641 ASP cc_start: 0.7768 (m-30) cc_final: 0.7450 (p0) REVERT: A 843 TRP cc_start: 0.7573 (m100) cc_final: 0.5297 (t-100) REVERT: A 953 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8360 (ttp80) REVERT: A 1021 LEU cc_start: 0.8560 (mt) cc_final: 0.8219 (mt) REVERT: A 1058 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8536 (mt) REVERT: A 1116 MET cc_start: 0.8055 (mmt) cc_final: 0.7772 (mmm) REVERT: A 1147 VAL cc_start: 0.8758 (t) cc_final: 0.8516 (m) REVERT: A 1268 SER cc_start: 0.8884 (t) cc_final: 0.8542 (p) REVERT: A 1308 MET cc_start: 0.4648 (tpt) cc_final: 0.4281 (tpt) outliers start: 36 outliers final: 26 residues processed: 144 average time/residue: 0.2102 time to fit residues: 44.0559 Evaluate side-chains 146 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 248 VAL Chi-restraints excluded: chain A residue 289 GLU 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 608 ILE Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 747 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 110 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 112 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.183924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134431 restraints weight = 11961.186| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.97 r_work: 0.3421 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9619 Z= 0.141 Angle : 0.562 9.927 13018 Z= 0.290 Chirality : 0.039 0.184 1528 Planarity : 0.004 0.050 1633 Dihedral : 4.188 29.230 1300 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.25 % Favored : 94.33 % Rotamer: Outliers : 3.58 % Allowed : 26.91 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1199 helix: 1.14 (0.19), residues: 767 sheet: -0.55 (1.26), residues: 24 loop : -1.06 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1097 HIS 0.011 0.001 HIS A 722 PHE 0.027 0.001 PHE A 739 TYR 0.014 0.001 TYR A1135 ARG 0.004 0.000 ARG A1373 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 559) hydrogen bonds : angle 4.44964 ( 1644) covalent geometry : bond 0.00318 ( 9619) covalent geometry : angle 0.56171 (13018) *********************** 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 152 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 1.031 Fit side-chains REVERT: A 109 CYS cc_start: 0.9198 (t) cc_final: 0.8448 (m) REVERT: A 138 LYS cc_start: 0.8649 (pttp) cc_final: 0.8407 (pttp) REVERT: A 156 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: A 229 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: A 330 TYR cc_start: 0.5331 (t80) cc_final: 0.2590 (t80) REVERT: A 333 MET cc_start: 0.8598 (mmp) cc_final: 0.8128 (mmp) REVERT: A 408 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8436 (mp) REVERT: A 438 THR cc_start: 0.8868 (p) cc_final: 0.8602 (p) REVERT: A 491 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 641 ASP cc_start: 0.7763 (m-30) cc_final: 0.7438 (p0) REVERT: A 843 TRP cc_start: 0.7561 (m100) cc_final: 0.5326 (t-100) REVERT: A 953 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8387 (ttp80) REVERT: A 1021 LEU cc_start: 0.8549 (mt) cc_final: 0.8229 (mt) REVERT: A 1058 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8485 (mt) REVERT: A 1116 MET cc_start: 0.8060 (mmt) cc_final: 0.7802 (mmm) REVERT: A 1147 VAL cc_start: 0.8682 (t) cc_final: 0.8450 (m) REVERT: A 1268 SER cc_start: 0.8840 (t) cc_final: 0.8502 (p) REVERT: A 1309 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8329 (ttpp) outliers start: 37 outliers final: 26 residues processed: 142 average time/residue: 0.1956 time to fit residues: 40.0983 Evaluate side-chains 144 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 182 SER Chi-restraints excluded: chain A residue 187 MET 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 408 ILE 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 722 HIS Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 747 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 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 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 97 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 HIS A1292 ASN ** 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 = 0.4167 r_free = 0.4167 target = 0.183463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.133750 restraints weight = 11797.648| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.03 r_work: 0.3426 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9619 Z= 0.153 Angle : 0.567 9.941 13018 Z= 0.293 Chirality : 0.040 0.179 1528 Planarity : 0.004 0.049 1633 Dihedral : 4.182 29.351 1300 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.25 % Favored : 94.33 % Rotamer: Outliers : 3.39 % Allowed : 27.20 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1199 helix: 1.12 (0.19), residues: 767 sheet: -0.62 (1.27), residues: 24 loop : -1.06 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1097 HIS 0.013 0.001 HIS A 722 PHE 0.030 0.001 PHE A 739 TYR 0.015 0.001 TYR A1135 ARG 0.004 0.000 ARG A1373 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 559) hydrogen bonds : angle 4.47394 ( 1644) covalent geometry : bond 0.00353 ( 9619) covalent geometry : angle 0.56707 (13018) *********************** 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 144 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 1.025 Fit side-chains REVERT: A 109 CYS cc_start: 0.9171 (t) cc_final: 0.8429 (m) REVERT: A 138 LYS cc_start: 0.8622 (pttp) cc_final: 0.8367 (pttp) REVERT: A 156 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: A 229 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: A 330 TYR cc_start: 0.5370 (t80) cc_final: 0.2473 (t80) REVERT: A 333 MET cc_start: 0.8602 (mmp) cc_final: 0.8134 (mmp) REVERT: A 408 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8433 (mp) REVERT: A 491 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 843 TRP cc_start: 0.7525 (m100) cc_final: 0.5332 (t-100) REVERT: A 953 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8393 (ttp80) REVERT: A 1021 LEU cc_start: 0.8564 (mt) cc_final: 0.8248 (mt) REVERT: A 1058 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8508 (mt) REVERT: A 1147 VAL cc_start: 0.8702 (t) cc_final: 0.8474 (m) REVERT: A 1252 LYS cc_start: 0.8491 (mttt) cc_final: 0.8149 (mttt) REVERT: A 1268 SER cc_start: 0.8845 (t) cc_final: 0.8516 (p) REVERT: A 1309 LYS cc_start: 0.8671 (ttpp) cc_final: 0.8330 (ttpp) outliers start: 35 outliers final: 26 residues processed: 138 average time/residue: 0.2065 time to fit residues: 41.0142 Evaluate side-chains 140 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 182 SER Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 228 THR 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 747 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 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 76 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.183837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.134763 restraints weight = 11921.727| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.01 r_work: 0.3423 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9619 Z= 0.137 Angle : 0.565 10.599 13018 Z= 0.289 Chirality : 0.039 0.181 1528 Planarity : 0.004 0.049 1633 Dihedral : 4.171 28.806 1300 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.34 % Favored : 94.25 % Rotamer: Outliers : 3.29 % Allowed : 27.69 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1199 helix: 1.12 (0.19), residues: 770 sheet: -0.65 (1.26), residues: 24 loop : -1.00 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1097 HIS 0.004 0.001 HIS A 767 PHE 0.031 0.001 PHE A 739 TYR 0.015 0.001 TYR A1135 ARG 0.005 0.000 ARG A1373 Details of bonding type rmsd hydrogen bonds : bond 0.04033 ( 559) hydrogen bonds : angle 4.43925 ( 1644) covalent geometry : bond 0.00309 ( 9619) covalent geometry : angle 0.56451 (13018) ********************** 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 146 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 1.089 Fit side-chains REVERT: A 109 CYS cc_start: 0.9168 (t) cc_final: 0.8413 (m) REVERT: A 138 LYS cc_start: 0.8653 (pttp) cc_final: 0.8405 (pttp) REVERT: A 156 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: A 229 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: A 330 TYR cc_start: 0.5208 (t80) cc_final: 0.2526 (t80) REVERT: A 333 MET cc_start: 0.8598 (mmp) cc_final: 0.8144 (mmp) REVERT: A 408 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8431 (mp) REVERT: A 491 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 641 ASP cc_start: 0.7809 (m-30) cc_final: 0.7476 (p0) REVERT: A 843 TRP cc_start: 0.7473 (m100) cc_final: 0.5283 (t-100) REVERT: A 953 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8403 (ttp80) REVERT: A 1021 LEU cc_start: 0.8549 (mt) cc_final: 0.8243 (mt) REVERT: A 1058 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8483 (mt) REVERT: A 1147 VAL cc_start: 0.8674 (t) cc_final: 0.8442 (m) REVERT: A 1268 SER cc_start: 0.8840 (t) cc_final: 0.8500 (p) REVERT: A 1309 LYS cc_start: 0.8694 (ttpp) cc_final: 0.8351 (ttpp) outliers start: 34 outliers final: 27 residues processed: 138 average time/residue: 0.2034 time to fit residues: 40.9258 Evaluate side-chains 143 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 182 SER Chi-restraints excluded: chain A residue 187 MET 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 678 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 747 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 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 27 optimal weight: 0.9990 chunk 74 optimal weight: 0.0040 chunk 54 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 6 optimal weight: 0.0270 chunk 18 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 0.4650 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.185130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136232 restraints weight = 11894.018| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.97 r_work: 0.3461 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9619 Z= 0.122 Angle : 0.550 11.006 13018 Z= 0.282 Chirality : 0.039 0.176 1528 Planarity : 0.004 0.051 1633 Dihedral : 4.085 27.677 1300 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.92 % Favored : 94.66 % Rotamer: Outliers : 3.10 % Allowed : 27.49 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1199 helix: 1.24 (0.19), residues: 764 sheet: -0.64 (1.27), residues: 24 loop : -1.03 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1097 HIS 0.003 0.001 HIS A 421 PHE 0.030 0.001 PHE A 739 TYR 0.013 0.001 TYR A1135 ARG 0.001 0.000 ARG A1101 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 559) hydrogen bonds : angle 4.36666 ( 1644) covalent geometry : bond 0.00268 ( 9619) covalent geometry : angle 0.55009 (13018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5359.32 seconds wall clock time: 93 minutes 23.58 seconds (5603.58 seconds total)