Starting phenix.real_space_refine on Sun Aug 4 03:31:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi4_37557/08_2024/8wi4_37557.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi4_37557/08_2024/8wi4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi4_37557/08_2024/8wi4_37557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi4_37557/08_2024/8wi4_37557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi4_37557/08_2024/8wi4_37557.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi4_37557/08_2024/8wi4_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 Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "A GLU 752": "OE1" <-> "OE2" Residue "A TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1196": "OE1" <-> "OE2" Residue "A GLU 1199": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.33, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 3.30 Conformation dependent library (CDL) restraints added in 1.5 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: 1.04 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: 3.07 Time building geometry restraints manager: 3.65 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: 98.38 - 105.57: 143 105.57 - 112.75: 5309 112.75 - 119.93: 3224 119.93 - 127.11: 4251 127.11 - 134.29: 91 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: 1.830 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.540 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.470 ------------------------------------------------------------------------------- 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= 0.163 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.061 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: 0.1513 time to fit residues: 30.8373 Evaluate side-chains 118 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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= 0.162 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 *********************** 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 fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 739 PHE cc_start: 0.8095 (t80) cc_final: 0.7889 (t80) REVERT: A 1058 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.7959 (mp) REVERT: A 1131 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7237 (pp) REVERT: A 1317 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6671 (tt) outliers start: 28 outliers final: 13 residues processed: 144 average time/residue: 0.1798 time to fit residues: 38.5303 Evaluate side-chains 130 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 33 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 87 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9619 Z= 0.244 Angle : 0.574 9.661 13018 Z= 0.302 Chirality : 0.040 0.145 1528 Planarity : 0.004 0.058 1633 Dihedral : 3.981 23.010 1301 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.34 % Favored : 95.25 % Rotamer: Outliers : 3.68 % Allowed : 28.36 % 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 (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: 0.69 (0.25), residues: 1199 helix: 1.32 (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 0.013 0.002 TRP A 878 HIS 0.005 0.001 HIS A 421 PHE 0.017 0.002 PHE A1014 TYR 0.018 0.001 TYR A1135 ARG 0.005 0.000 ARG A1335 *********************** 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 173 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 109 CYS cc_start: 0.8547 (t) cc_final: 0.7842 (m) REVERT: A 330 TYR cc_start: 0.5134 (t80) cc_final: 0.2382 (t80) REVERT: A 408 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8566 (mp) REVERT: A 608 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7928 (tp) REVERT: A 953 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7925 (ttp80) REVERT: A 1058 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8436 (mt) REVERT: A 1268 SER cc_start: 0.8598 (t) cc_final: 0.8313 (p) REVERT: A 1308 MET cc_start: 0.5636 (tpt) cc_final: 0.5175 (tpt) outliers start: 38 outliers final: 15 residues processed: 164 average time/residue: 0.2069 time to fit residues: 48.5689 Evaluate side-chains 143 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 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 107 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 57 optimal weight: 0.3980 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 243 ASN A 722 HIS A 869 ASN ** A1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2969 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= 0.214 Angle : 0.538 9.158 13018 Z= 0.284 Chirality : 0.039 0.136 1528 Planarity : 0.004 0.055 1633 Dihedral : 3.987 25.439 1300 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.92 % Favored : 94.66 % Rotamer: Outliers : 3.87 % Allowed : 27.88 % Favored : 68.25 % 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: 0.66 (0.25), residues: 1199 helix: 1.30 (0.19), residues: 761 sheet: -0.94 (1.15), 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 0.009 0.001 HIS A 722 PHE 0.013 0.001 PHE A1157 TYR 0.013 0.001 TYR A1135 ARG 0.003 0.000 ARG A1346 *********************** 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 165 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 109 CYS cc_start: 0.8476 (t) cc_final: 0.7728 (m) REVERT: A 229 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: A 330 TYR cc_start: 0.5055 (t80) cc_final: 0.2416 (t80) REVERT: A 333 MET cc_start: 0.8493 (mmp) cc_final: 0.8148 (mmp) REVERT: A 408 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8602 (mp) REVERT: A 771 MET cc_start: 0.7893 (mmm) cc_final: 0.7651 (mmm) REVERT: A 953 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7923 (ttp80) REVERT: A 1058 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8415 (mt) outliers start: 40 outliers final: 23 residues processed: 154 average time/residue: 0.2237 time to fit residues: 50.9478 Evaluate side-chains 147 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 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 747 LEU Chi-restraints excluded: chain A residue 767 HIS 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 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 96 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** A 722 HIS A 869 ASN ** A1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3333 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= 0.297 Angle : 0.591 9.293 13018 Z= 0.308 Chirality : 0.041 0.150 1528 Planarity : 0.004 0.053 1633 Dihedral : 4.125 28.322 1300 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.00 % Favored : 94.58 % Rotamer: Outliers : 3.48 % Allowed : 28.46 % 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: 0.46 (0.25), residues: 1199 helix: 1.08 (0.19), residues: 766 sheet: -0.79 (1.20), residues: 24 loop : -1.06 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1097 HIS 0.019 0.001 HIS A 722 PHE 0.025 0.002 PHE A 739 TYR 0.017 0.001 TYR A1135 ARG 0.004 0.000 ARG A1346 *********************** 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 157 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 121 time to evaluate : 0.956 Fit side-chains REVERT: A 109 CYS cc_start: 0.8701 (t) cc_final: 0.8000 (m) REVERT: A 156 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: A 229 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: A 330 TYR cc_start: 0.5249 (t80) cc_final: 0.2351 (t80) REVERT: A 333 MET cc_start: 0.8537 (mmp) cc_final: 0.8157 (mmp) REVERT: A 408 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8617 (mp) REVERT: A 608 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7906 (tp) REVERT: A 641 ASP cc_start: 0.6710 (p0) cc_final: 0.6500 (m-30) REVERT: A 843 TRP cc_start: 0.7295 (m100) cc_final: 0.5695 (t-100) REVERT: A 1058 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8505 (mt) outliers start: 36 outliers final: 21 residues processed: 148 average time/residue: 0.1989 time to fit residues: 41.9880 Evaluate side-chains 142 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 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 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 1315 LEU 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 39 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 116 optimal weight: 0.1980 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9619 Z= 0.202 Angle : 0.546 9.279 13018 Z= 0.284 Chirality : 0.039 0.145 1528 Planarity : 0.004 0.052 1633 Dihedral : 4.092 27.991 1300 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.75 % Favored : 94.83 % Rotamer: Outliers : 3.39 % Allowed : 28.36 % Favored : 68.25 % 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: 0.55 (0.25), residues: 1199 helix: 1.16 (0.19), residues: 766 sheet: -0.71 (1.21), residues: 24 loop : -1.04 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1097 HIS 0.006 0.001 HIS A 97 PHE 0.024 0.001 PHE A 739 TYR 0.026 0.001 TYR A1135 ARG 0.007 0.000 ARG A 953 *********************** 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 154 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 1.056 Fit side-chains REVERT: A 109 CYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7988 (m) REVERT: A 156 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: A 229 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: A 330 TYR cc_start: 0.5253 (t80) cc_final: 0.2319 (t80) REVERT: A 333 MET cc_start: 0.8535 (mmp) cc_final: 0.8149 (mmp) REVERT: A 408 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8590 (mp) REVERT: A 438 THR cc_start: 0.9075 (p) cc_final: 0.8833 (p) REVERT: A 641 ASP cc_start: 0.6757 (p0) cc_final: 0.6554 (m-30) REVERT: A 843 TRP cc_start: 0.7316 (m100) cc_final: 0.5592 (t-100) REVERT: A 1058 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8410 (mt) outliers start: 35 outliers final: 22 residues processed: 144 average time/residue: 0.1854 time to fit residues: 39.0686 Evaluate side-chains 144 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 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 750 CYS Chi-restraints excluded: chain A residue 767 HIS Chi-restraints excluded: chain A residue 872 SER 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 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 111 optimal weight: 0.3980 chunk 13 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 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 722 HIS ** A1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3415 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= 0.173 Angle : 0.529 8.992 13018 Z= 0.275 Chirality : 0.038 0.167 1528 Planarity : 0.004 0.051 1633 Dihedral : 4.031 27.210 1300 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.59 % Favored : 95.00 % Rotamer: Outliers : 3.29 % Allowed : 27.88 % 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 (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: 0.66 (0.25), residues: 1199 helix: 1.28 (0.19), residues: 760 sheet: -0.54 (1.25), residues: 24 loop : -1.06 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1097 HIS 0.010 0.001 HIS A 722 PHE 0.026 0.001 PHE A 739 TYR 0.009 0.001 TYR A 627 ARG 0.005 0.000 ARG A 953 *********************** 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 155 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 1.106 Fit side-chains REVERT: A 109 CYS cc_start: 0.8652 (t) cc_final: 0.7960 (m) REVERT: A 156 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: A 229 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: A 330 TYR cc_start: 0.5067 (t80) cc_final: 0.2475 (t80) REVERT: A 333 MET cc_start: 0.8482 (mmp) cc_final: 0.8104 (mmp) REVERT: A 408 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8571 (mp) REVERT: A 438 THR cc_start: 0.9073 (p) cc_final: 0.8847 (p) REVERT: A 843 TRP cc_start: 0.7274 (m100) cc_final: 0.5583 (t-100) REVERT: A 1058 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8414 (mt) REVERT: A 1268 SER cc_start: 0.8624 (t) cc_final: 0.8324 (p) REVERT: A 1309 LYS cc_start: 0.8601 (ttpp) cc_final: 0.8297 (ttpp) outliers start: 34 outliers final: 23 residues processed: 148 average time/residue: 0.1873 time to fit residues: 40.5127 Evaluate side-chains 144 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 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 678 ILE 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 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 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 71 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 78 optimal weight: 0.0980 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.0000 chunk 105 optimal weight: 0.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 869 ASN ** A1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 9619 Z= 0.161 Angle : 0.531 9.412 13018 Z= 0.274 Chirality : 0.038 0.158 1528 Planarity : 0.004 0.050 1633 Dihedral : 4.011 26.373 1300 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.92 % Favored : 94.66 % Rotamer: Outliers : 3.10 % Allowed : 28.36 % 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: 0.71 (0.25), residues: 1199 helix: 1.33 (0.19), residues: 760 sheet: -0.51 (1.27), residues: 24 loop : -1.05 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1097 HIS 0.003 0.001 HIS A 421 PHE 0.026 0.001 PHE A 739 TYR 0.008 0.001 TYR A 627 ARG 0.006 0.000 ARG A 953 *********************** 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 149 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 1.014 Fit side-chains REVERT: A 109 CYS cc_start: 0.8660 (OUTLIER) cc_final: 0.7961 (m) REVERT: A 156 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: A 229 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: A 330 TYR cc_start: 0.5145 (t80) cc_final: 0.2541 (t80) REVERT: A 333 MET cc_start: 0.8493 (mmp) cc_final: 0.8129 (mmp) REVERT: A 408 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8594 (mp) REVERT: A 739 PHE cc_start: 0.8190 (t80) cc_final: 0.7986 (t80) REVERT: A 843 TRP cc_start: 0.7225 (m100) cc_final: 0.5536 (t-100) REVERT: A 957 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7771 (ttp80) REVERT: A 1058 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8364 (mt) REVERT: A 1309 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8304 (ttpp) outliers start: 32 outliers final: 22 residues processed: 141 average time/residue: 0.1918 time to fit residues: 39.4962 Evaluate side-chains 141 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 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 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 869 ASN Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 957 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 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 110 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 0.0670 chunk 69 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 869 ASN ** A1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3468 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= 0.185 Angle : 0.544 10.471 13018 Z= 0.280 Chirality : 0.039 0.151 1528 Planarity : 0.004 0.049 1633 Dihedral : 4.019 26.446 1300 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.84 % Favored : 94.75 % Rotamer: Outliers : 3.19 % Allowed : 27.98 % 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 (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: 1.30 (0.19), residues: 765 sheet: -0.45 (1.28), residues: 24 loop : -1.01 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1097 HIS 0.005 0.001 HIS A 767 PHE 0.026 0.001 PHE A 739 TYR 0.009 0.001 TYR A 627 ARG 0.005 0.000 ARG A 953 *********************** 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 146 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 1.089 Fit side-chains REVERT: A 109 CYS cc_start: 0.8656 (OUTLIER) cc_final: 0.7964 (m) REVERT: A 156 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: A 229 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: A 330 TYR cc_start: 0.5220 (t80) cc_final: 0.2646 (t80) REVERT: A 333 MET cc_start: 0.8498 (mmp) cc_final: 0.8121 (mmp) REVERT: A 408 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 438 THR cc_start: 0.9066 (p) cc_final: 0.8839 (p) REVERT: A 739 PHE cc_start: 0.8174 (t80) cc_final: 0.7959 (t80) REVERT: A 843 TRP cc_start: 0.7234 (m100) cc_final: 0.5546 (t-100) REVERT: A 1058 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8368 (mt) REVERT: A 1309 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8304 (ttpp) outliers start: 33 outliers final: 24 residues processed: 140 average time/residue: 0.2029 time to fit residues: 41.2644 Evaluate side-chains 141 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 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 444 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 590 LEU 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 750 CYS Chi-restraints excluded: chain A residue 767 HIS Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 872 SER 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 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 54 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 95 optimal weight: 0.0370 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 869 ASN ** A1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9619 Z= 0.191 Angle : 0.553 10.932 13018 Z= 0.284 Chirality : 0.039 0.197 1528 Planarity : 0.004 0.049 1633 Dihedral : 4.044 26.686 1300 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.34 % Favored : 94.25 % Rotamer: Outliers : 3.10 % Allowed : 28.27 % 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 (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: 0.69 (0.25), residues: 1199 helix: 1.27 (0.19), residues: 766 sheet: -0.47 (1.28), residues: 24 loop : -1.01 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1097 HIS 0.005 0.001 HIS A 767 PHE 0.025 0.001 PHE A 739 TYR 0.009 0.001 TYR A 627 ARG 0.005 0.000 ARG A 953 ********************** 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 143 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 1.025 Fit side-chains REVERT: A 109 CYS cc_start: 0.8659 (OUTLIER) cc_final: 0.7984 (m) REVERT: A 156 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7464 (tt0) REVERT: A 229 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: A 330 TYR cc_start: 0.5263 (t80) cc_final: 0.2729 (t80) REVERT: A 333 MET cc_start: 0.8492 (mmp) cc_final: 0.8105 (mmp) REVERT: A 408 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8575 (mp) REVERT: A 438 THR cc_start: 0.9071 (p) cc_final: 0.8845 (p) REVERT: A 739 PHE cc_start: 0.8224 (t80) cc_final: 0.7999 (t80) REVERT: A 843 TRP cc_start: 0.7193 (m100) cc_final: 0.5566 (t-100) REVERT: A 1058 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8378 (mt) REVERT: A 1268 SER cc_start: 0.8682 (t) cc_final: 0.8388 (p) REVERT: A 1309 LYS cc_start: 0.8661 (ttpp) cc_final: 0.8370 (ttpp) outliers start: 32 outliers final: 24 residues processed: 137 average time/residue: 0.2109 time to fit residues: 42.2899 Evaluate side-chains 139 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 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 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 750 CYS Chi-restraints excluded: chain A residue 767 HIS Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 872 SER 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 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 87 optimal weight: 0.0970 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 0.0040 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 869 ASN ** A1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4194 r_free = 0.4194 target = 0.186105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.136675 restraints weight = 11759.470| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.99 r_work: 0.3467 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9619 Z= 0.175 Angle : 0.552 10.760 13018 Z= 0.286 Chirality : 0.039 0.195 1528 Planarity : 0.004 0.048 1633 Dihedral : 4.033 26.372 1300 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.84 % Favored : 94.75 % Rotamer: Outliers : 3.29 % Allowed : 27.78 % Favored : 68.93 % 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: 1.35 (0.19), residues: 760 sheet: -0.50 (1.27), residues: 24 loop : -1.04 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1097 HIS 0.005 0.001 HIS A 767 PHE 0.023 0.001 PHE A 739 TYR 0.009 0.001 TYR A 627 ARG 0.005 0.000 ARG A 953 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2200.37 seconds wall clock time: 40 minutes 18.65 seconds (2418.65 seconds total)