Starting phenix.real_space_refine on Fri Jan 17 23:16:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rq3_19431/01_2025/8rq3_19431.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rq3_19431/01_2025/8rq3_19431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rq3_19431/01_2025/8rq3_19431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rq3_19431/01_2025/8rq3_19431.map" model { file = "/net/cci-nas-00/data/ceres_data/8rq3_19431/01_2025/8rq3_19431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rq3_19431/01_2025/8rq3_19431.cif" } resolution = 3.21 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= 0.000 sd= 0.017 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 50 5.16 5 C 7362 2.51 5 N 1923 2.21 5 O 2040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11375 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1432, 11375 Classifications: {'peptide': 1432} Link IDs: {'PTRANS': 42, 'TRANS': 1389} Chain breaks: 3 Time building chain proxies: 7.36, per 1000 atoms: 0.65 Number of scatterers: 11375 At special positions: 0 Unit cell: (105.78, 135.45, 148.995, 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 50 16.00 O 2040 8.00 N 1923 7.00 C 7362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 25 " distance=2.03 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: 2.87 Conformation dependent library (CDL) restraints added in 1.5 seconds 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2698 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 7 sheets defined 69.9% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.719A pdb=" N CYS A 5 " --> pdb=" O ASP A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 51 removed outlier: 4.599A pdb=" N VAL A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Proline residue: A 35 - end of helix removed outlier: 3.678A pdb=" N LEU A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Proline residue: A 44 - end of helix Processing helix chain 'A' and resid 61 through 90 Processing helix chain 'A' and resid 100 through 118 removed outlier: 3.705A pdb=" N HIS A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 128 through 155 removed outlier: 3.666A pdb=" N VAL A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLN A 145 " --> pdb=" O CYS A 141 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 183 removed outlier: 3.539A pdb=" N SER A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 208 through 218 removed outlier: 3.832A pdb=" N LEU A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 265 removed outlier: 4.806A pdb=" N LYS A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASP A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 332 removed outlier: 6.643A pdb=" N VAL A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'A' and resid 353 through 401 removed outlier: 3.997A pdb=" N TYR A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 358 " --> pdb=" O TRP A 354 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N CYS A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 412 through 422 Processing helix chain 'A' and resid 422 through 433 Processing helix chain 'A' and resid 435 through 456 removed outlier: 4.546A pdb=" N VAL A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 504 removed outlier: 4.116A pdb=" N GLY A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE A 470 " --> pdb=" O MET A 466 " (cutoff:3.500A) Proline residue: A 471 - end of helix Processing helix chain 'A' and resid 504 through 511 Processing helix chain 'A' and resid 513 through 564 Proline residue: A 550 - end of helix Processing helix chain 'A' and resid 571 through 586 Processing helix chain 'A' and resid 587 through 613 Proline residue: A 593 - end of helix removed outlier: 3.808A pdb=" N VAL A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 682 removed outlier: 3.507A pdb=" N GLY A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 717 Processing helix chain 'A' and resid 722 through 733 Processing helix chain 'A' and resid 735 through 742 Processing helix chain 'A' and resid 758 through 774 removed outlier: 3.772A pdb=" N ASP A 774 " --> pdb=" O ALA A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 800 Processing helix chain 'A' and resid 820 through 824 Processing helix chain 'A' and resid 840 through 847 Processing helix chain 'A' and resid 849 through 858 removed outlier: 3.727A pdb=" N ARG A 853 " --> pdb=" O GLY A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 861 No H-bonds generated for 'chain 'A' and resid 859 through 861' Processing helix chain 'A' and resid 900 through 912 removed outlier: 3.603A pdb=" N LEU A 905 " --> pdb=" O ARG A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.098A pdb=" N TYR A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 998 removed outlier: 3.686A pdb=" N ASN A 985 " --> pdb=" O PHE A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1004 removed outlier: 3.645A pdb=" N ASP A1002 " --> pdb=" O TRP A 999 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A1003 " --> pdb=" O THR A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1011 removed outlier: 3.829A pdb=" N ASN A1011 " --> pdb=" O GLY A1008 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1008 through 1011' Processing helix chain 'A' and resid 1012 through 1061 Processing helix chain 'A' and resid 1064 through 1071 removed outlier: 3.851A pdb=" N PHE A1068 " --> pdb=" O PRO A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1082 removed outlier: 3.558A pdb=" N ILE A1076 " --> pdb=" O PRO A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1089 Processing helix chain 'A' and resid 1089 through 1116 removed outlier: 3.895A pdb=" N GLN A1093 " --> pdb=" O ASP A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1121 Processing helix chain 'A' and resid 1122 through 1165 removed outlier: 3.794A pdb=" N LEU A1126 " --> pdb=" O ILE A1122 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN A1143 " --> pdb=" O ALA A1139 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) Proline residue: A1154 - end of helix Processing helix chain 'A' and resid 1165 through 1173 Processing helix chain 'A' and resid 1174 through 1225 removed outlier: 3.580A pdb=" N PHE A1178 " --> pdb=" O HIS A1174 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N CYS A1192 " --> pdb=" O ILE A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1242 removed outlier: 3.631A pdb=" N VAL A1234 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN A1240 " --> pdb=" O PHE A1236 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A1242 " --> pdb=" O LEU A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1262 Processing helix chain 'A' and resid 1262 through 1273 removed outlier: 3.543A pdb=" N ASN A1273 " --> pdb=" O SER A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1343 removed outlier: 4.037A pdb=" N LEU A1339 " --> pdb=" O GLY A1335 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR A1340 " --> pdb=" O LYS A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1364 No H-bonds generated for 'chain 'A' and resid 1362 through 1364' Processing helix chain 'A' and resid 1365 through 1372 removed outlier: 3.971A pdb=" N ARG A1372 " --> pdb=" O ASP A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1392 Processing helix chain 'A' and resid 1398 through 1409 Processing helix chain 'A' and resid 1411 through 1416 Processing helix chain 'A' and resid 1434 through 1450 Processing helix chain 'A' and resid 1464 through 1479 Processing helix chain 'A' and resid 1490 through 1494 removed outlier: 3.827A pdb=" N THR A1493 " --> pdb=" O ARG A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1513 through 1519 removed outlier: 4.120A pdb=" N SER A1519 " --> pdb=" O GLU A1515 " (cutoff:3.500A) Processing helix chain 'A' and resid 1522 through 1528 Processing sheet with id=AA1, first strand: chain 'A' and resid 623 through 626 removed outlier: 5.892A pdb=" N ARG A 624 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ASN A 686 " --> pdb=" O PHE A 640 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE A 640 " --> pdb=" O ASN A 686 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N HIS A 688 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA A 638 " --> pdb=" O HIS A 688 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL A 653 " --> pdb=" O GLU A 637 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER A 639 " --> pdb=" O GLN A 651 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN A 651 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 697 through 700 removed outlier: 6.578A pdb=" N ALA A 698 " --> pdb=" O ILE A 779 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 663 " --> pdb=" O PHE A 813 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA A 664 " --> pdb=" O VAL A 828 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU A 830 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 666 " --> pdb=" O LEU A 830 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE A 827 " --> pdb=" O LYS A 838 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS A 838 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A 829 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 709 through 710 Processing sheet with id=AA4, first strand: chain 'A' and resid 1313 through 1316 removed outlier: 5.918A pdb=" N LYS A1314 " --> pdb=" O VAL A1303 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL A1303 " --> pdb=" O LYS A1314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1313 through 1316 removed outlier: 5.918A pdb=" N LYS A1314 " --> pdb=" O VAL A1303 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL A1303 " --> pdb=" O LYS A1314 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE A1298 " --> pdb=" O ILE A1355 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A1355 " --> pdb=" O PHE A1298 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASN A1300 " --> pdb=" O GLN A1353 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLN A1353 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1375 through 1376 removed outlier: 6.273A pdb=" N ILE A1376 " --> pdb=" O ASP A1457 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU A1454 " --> pdb=" O ILE A1485 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE A1487 " --> pdb=" O LEU A1454 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU A1456 " --> pdb=" O ILE A1487 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LYS A1325 " --> pdb=" O LYS A1499 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N MET A1501 " --> pdb=" O LYS A1325 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY A1327 " --> pdb=" O MET A1501 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU A1503 " --> pdb=" O GLY A1327 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL A1329 " --> pdb=" O LEU A1503 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1385 through 1386 736 hydrogen bonds defined for protein. 2151 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: 4.50 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3416 1.33 - 1.45: 1705 1.45 - 1.57: 6409 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 11610 Sorted by residual: bond pdb=" CG LEU A 74 " pdb=" CD2 LEU A 74 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 6.02e+00 bond pdb=" CG1 ILE A1042 " pdb=" CD1 ILE A1042 " ideal model delta sigma weight residual 1.513 1.425 0.088 3.90e-02 6.57e+02 5.14e+00 bond pdb=" CB ILE A 203 " pdb=" CG2 ILE A 203 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.58e+00 bond pdb=" CG1 ILE A 318 " pdb=" CD1 ILE A 318 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.85e+00 bond pdb=" CB VAL A 212 " pdb=" CG1 VAL A 212 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.77e+00 ... (remaining 11605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 15127 1.82 - 3.63: 514 3.63 - 5.45: 70 5.45 - 7.27: 21 7.27 - 9.08: 6 Bond angle restraints: 15738 Sorted by residual: angle pdb=" C ARG A 918 " pdb=" N ARG A 919 " pdb=" CA ARG A 919 " ideal model delta sigma weight residual 122.05 115.35 6.70 1.48e+00 4.57e-01 2.05e+01 angle pdb=" N GLN A1134 " pdb=" CA GLN A1134 " pdb=" CB GLN A1134 " ideal model delta sigma weight residual 110.16 115.26 -5.10 1.48e+00 4.57e-01 1.19e+01 angle pdb=" N GLY A 920 " pdb=" CA GLY A 920 " pdb=" C GLY A 920 " ideal model delta sigma weight residual 113.18 105.62 7.56 2.37e+00 1.78e-01 1.02e+01 angle pdb=" C ARG A1438 " pdb=" N GLN A1439 " pdb=" CA GLN A1439 " ideal model delta sigma weight residual 120.72 115.63 5.09 1.67e+00 3.59e-01 9.31e+00 angle pdb=" C ASN A1299 " pdb=" N ASN A1300 " pdb=" CA ASN A1300 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.59e+00 ... (remaining 15733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6159 17.76 - 35.52: 636 35.52 - 53.28: 103 53.28 - 71.04: 19 71.04 - 88.80: 10 Dihedral angle restraints: 6927 sinusoidal: 2761 harmonic: 4166 Sorted by residual: dihedral pdb=" CA THR A 815 " pdb=" C THR A 815 " pdb=" N HIS A 816 " pdb=" CA HIS A 816 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA SER A 189 " pdb=" C SER A 189 " pdb=" N THR A 190 " pdb=" CA THR A 190 " ideal model delta harmonic sigma weight residual 180.00 -161.14 -18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLY A 356 " pdb=" C GLY A 356 " pdb=" N TYR A 357 " pdb=" CA TYR A 357 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 6924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1057 0.038 - 0.076: 579 0.076 - 0.114: 147 0.114 - 0.152: 52 0.152 - 0.190: 7 Chirality restraints: 1842 Sorted by residual: chirality pdb=" CA GLU A 514 " pdb=" N GLU A 514 " pdb=" C GLU A 514 " pdb=" CB GLU A 514 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CA ARG A 919 " pdb=" N ARG A 919 " pdb=" C ARG A 919 " pdb=" CB ARG A 919 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CB ILE A 307 " pdb=" CA ILE A 307 " pdb=" CG1 ILE A 307 " pdb=" CG2 ILE A 307 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 1839 not shown) Planarity restraints: 1949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 63 " 0.023 2.00e-02 2.50e+03 2.21e-02 8.55e+00 pdb=" CG PHE A 63 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A 63 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 63 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 63 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 63 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 63 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 919 " 0.011 2.00e-02 2.50e+03 2.32e-02 5.36e+00 pdb=" C ARG A 919 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG A 919 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY A 920 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1124 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A1125 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A1125 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1125 " 0.031 5.00e-02 4.00e+02 ... (remaining 1946 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 346 2.70 - 3.25: 12090 3.25 - 3.80: 18368 3.80 - 4.35: 22873 4.35 - 4.90: 38974 Nonbonded interactions: 92651 Sorted by model distance: nonbonded pdb=" N VAL A 958 " pdb=" OE1 GLU A1259 " model vdw 2.149 3.120 nonbonded pdb=" OG SER A1049 " pdb=" OD1 ASP A1088 " model vdw 2.206 3.040 nonbonded pdb=" NE2 GLN A 661 " pdb=" OD1 ASP A 825 " model vdw 2.208 3.120 nonbonded pdb=" O THR A1317 " pdb=" OH TYR A1511 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASN A 405 " pdb=" NH2 ARG A 408 " model vdw 2.249 3.120 ... (remaining 92646 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: 5.500 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: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.120 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 : 0.009 0.088 11610 Z= 0.591 Angle : 0.806 9.084 15738 Z= 0.437 Chirality : 0.050 0.190 1842 Planarity : 0.005 0.054 1949 Dihedral : 14.581 88.798 4226 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.22), residues: 1424 helix: 0.51 (0.17), residues: 924 sheet: -1.24 (0.65), residues: 66 loop : -1.66 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 45 HIS 0.007 0.001 HIS A1367 PHE 0.051 0.003 PHE A 63 TYR 0.032 0.002 TYR A 48 ARG 0.010 0.001 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.166 Fit side-chains REVERT: A 52 ARG cc_start: 0.7498 (ptp-170) cc_final: 0.7184 (ptp-170) REVERT: A 763 GLN cc_start: 0.7642 (mt0) cc_final: 0.7429 (tt0) REVERT: A 806 LEU cc_start: 0.7692 (mp) cc_final: 0.7168 (mp) REVERT: A 811 ARG cc_start: 0.7097 (ptt180) cc_final: 0.6716 (ptt180) REVERT: A 1280 TRP cc_start: 0.8122 (m-10) cc_final: 0.7724 (m-10) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2560 time to fit residues: 46.8806 Evaluate side-chains 107 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.0270 chunk 68 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 145 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN A1059 ASN ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.195965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.114959 restraints weight = 12439.080| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.11 r_work: 0.2984 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11610 Z= 0.197 Angle : 0.565 7.920 15738 Z= 0.295 Chirality : 0.041 0.150 1842 Planarity : 0.004 0.045 1949 Dihedral : 4.288 22.944 1541 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.79 % Allowed : 7.41 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1424 helix: 1.33 (0.17), residues: 946 sheet: -0.99 (0.63), residues: 67 loop : -1.72 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 226 HIS 0.007 0.001 HIS A 794 PHE 0.024 0.002 PHE A1236 TYR 0.019 0.001 TYR A 48 ARG 0.005 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6469 (mmm) cc_final: 0.5054 (ppp) REVERT: A 52 ARG cc_start: 0.6953 (ptp-170) cc_final: 0.6615 (ptp-170) REVERT: A 203 ILE cc_start: 0.8054 (mm) cc_final: 0.7246 (pt) REVERT: A 500 GLU cc_start: 0.7109 (tp30) cc_final: 0.6578 (pt0) REVERT: A 634 LYS cc_start: 0.6358 (OUTLIER) cc_final: 0.6119 (ttpp) REVERT: A 1284 LYS cc_start: 0.8330 (tptp) cc_final: 0.7455 (tmtt) outliers start: 10 outliers final: 2 residues processed: 125 average time/residue: 0.2778 time to fit residues: 51.6367 Evaluate side-chains 114 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 1369 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 87 optimal weight: 0.0370 chunk 133 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 986 ASN A1367 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.196350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.128434 restraints weight = 12554.433| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.27 r_work: 0.3011 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11610 Z= 0.183 Angle : 0.521 7.729 15738 Z= 0.270 Chirality : 0.040 0.142 1842 Planarity : 0.003 0.044 1949 Dihedral : 3.968 20.764 1541 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.50 % Allowed : 11.36 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.23), residues: 1424 helix: 1.73 (0.17), residues: 944 sheet: -0.59 (0.63), residues: 67 loop : -1.58 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1202 HIS 0.004 0.001 HIS A1367 PHE 0.018 0.001 PHE A1236 TYR 0.014 0.001 TYR A 48 ARG 0.004 0.000 ARG A 811 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6535 (mmm) cc_final: 0.5354 (ppp) REVERT: A 52 ARG cc_start: 0.6980 (ptp-170) cc_final: 0.6712 (ptp-170) REVERT: A 137 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6913 (mp) REVERT: A 203 ILE cc_start: 0.8102 (mm) cc_final: 0.7313 (pt) REVERT: A 300 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8087 (t0) REVERT: A 500 GLU cc_start: 0.7234 (tp30) cc_final: 0.6811 (tp30) REVERT: A 634 LYS cc_start: 0.6411 (OUTLIER) cc_final: 0.6168 (ttpp) REVERT: A 688 HIS cc_start: 0.7085 (t70) cc_final: 0.6559 (t70) REVERT: A 1207 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8271 (mt) REVERT: A 1280 TRP cc_start: 0.7964 (m-10) cc_final: 0.7238 (m-10) REVERT: A 1304 ARG cc_start: 0.6668 (ttm110) cc_final: 0.6452 (ttm110) outliers start: 19 outliers final: 10 residues processed: 132 average time/residue: 0.2484 time to fit residues: 47.6293 Evaluate side-chains 124 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 993 ASN Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1439 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 5 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 28 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 986 ASN A1390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.196991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115886 restraints weight = 12471.123| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.12 r_work: 0.2956 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11610 Z= 0.194 Angle : 0.512 8.295 15738 Z= 0.265 Chirality : 0.040 0.139 1842 Planarity : 0.003 0.045 1949 Dihedral : 3.858 21.735 1541 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.97 % Allowed : 13.25 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.28 (0.23), residues: 1424 helix: 1.92 (0.17), residues: 939 sheet: -0.31 (0.64), residues: 67 loop : -1.50 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1202 HIS 0.003 0.001 HIS A1053 PHE 0.018 0.001 PHE A1236 TYR 0.013 0.001 TYR A 48 ARG 0.002 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6474 (mmm) cc_final: 0.5364 (ppp) REVERT: A 137 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6854 (mp) REVERT: A 203 ILE cc_start: 0.8022 (mm) cc_final: 0.7194 (pt) REVERT: A 300 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8078 (t0) REVERT: A 500 GLU cc_start: 0.7174 (tp30) cc_final: 0.6728 (tp30) REVERT: A 634 LYS cc_start: 0.6320 (OUTLIER) cc_final: 0.6098 (ttpp) REVERT: A 688 HIS cc_start: 0.7141 (t70) cc_final: 0.6709 (t70) REVERT: A 763 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7061 (tt0) REVERT: A 1207 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8181 (mt) REVERT: A 1280 TRP cc_start: 0.7761 (m-10) cc_final: 0.7401 (m-10) outliers start: 25 outliers final: 14 residues processed: 133 average time/residue: 0.2427 time to fit residues: 47.8836 Evaluate side-chains 128 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 993 ASN Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1293 HIS Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1439 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 138 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 136 optimal weight: 30.0000 chunk 76 optimal weight: 8.9990 chunk 129 optimal weight: 0.9990 chunk 97 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS A 986 ASN A1341 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.195047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120569 restraints weight = 12378.057| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.86 r_work: 0.3004 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11610 Z= 0.191 Angle : 0.505 8.286 15738 Z= 0.261 Chirality : 0.040 0.138 1842 Planarity : 0.003 0.046 1949 Dihedral : 3.775 20.814 1541 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.81 % Allowed : 14.12 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.48 (0.23), residues: 1424 helix: 2.07 (0.17), residues: 938 sheet: -0.02 (0.65), residues: 67 loop : -1.44 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1202 HIS 0.003 0.001 HIS A 688 PHE 0.017 0.001 PHE A1236 TYR 0.012 0.001 TYR A 48 ARG 0.002 0.000 ARG A1304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6565 (mmm) cc_final: 0.5507 (ppp) REVERT: A 52 ARG cc_start: 0.6889 (ptp-170) cc_final: 0.6619 (ptp-170) REVERT: A 63 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.6348 (t80) REVERT: A 203 ILE cc_start: 0.8247 (mm) cc_final: 0.7466 (pt) REVERT: A 300 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8135 (t0) REVERT: A 500 GLU cc_start: 0.7507 (tp30) cc_final: 0.7025 (tp30) REVERT: A 634 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.6344 (ttpp) REVERT: A 688 HIS cc_start: 0.7243 (t70) cc_final: 0.6810 (t70) REVERT: A 763 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7268 (tt0) REVERT: A 1207 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8427 (mt) REVERT: A 1276 ASN cc_start: 0.8911 (m-40) cc_final: 0.8679 (m-40) REVERT: A 1280 TRP cc_start: 0.7804 (m-10) cc_final: 0.7561 (m-10) REVERT: A 1304 ARG cc_start: 0.6864 (ttm110) cc_final: 0.6569 (ttm110) REVERT: A 1501 MET cc_start: 0.4994 (mmp) cc_final: 0.3528 (ttt) REVERT: A 1507 LYS cc_start: 0.7694 (mmmt) cc_final: 0.7479 (mttm) outliers start: 23 outliers final: 14 residues processed: 131 average time/residue: 0.2273 time to fit residues: 45.0212 Evaluate side-chains 129 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 993 ASN Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1293 HIS Chi-restraints excluded: chain A residue 1341 ASN Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1439 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 33 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 117 optimal weight: 0.0570 chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 113 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 986 ASN A1185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.198075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128221 restraints weight = 12547.692| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.78 r_work: 0.3088 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11610 Z= 0.160 Angle : 0.493 8.555 15738 Z= 0.253 Chirality : 0.039 0.137 1842 Planarity : 0.003 0.045 1949 Dihedral : 3.688 21.209 1541 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.13 % Allowed : 14.35 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.65 (0.23), residues: 1424 helix: 2.22 (0.17), residues: 940 sheet: -0.05 (0.65), residues: 67 loop : -1.41 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1202 HIS 0.003 0.001 HIS A 688 PHE 0.015 0.001 PHE A 851 TYR 0.012 0.001 TYR A 48 ARG 0.001 0.000 ARG A1096 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6480 (mmm) cc_final: 0.5500 (ppp) REVERT: A 63 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6221 (t80) REVERT: A 203 ILE cc_start: 0.8127 (mm) cc_final: 0.7330 (pt) REVERT: A 300 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8109 (t0) REVERT: A 500 GLU cc_start: 0.7303 (tp30) cc_final: 0.6848 (tp30) REVERT: A 634 LYS cc_start: 0.6475 (OUTLIER) cc_final: 0.6233 (ttpp) REVERT: A 763 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7109 (tt0) REVERT: A 1207 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8292 (mt) REVERT: A 1276 ASN cc_start: 0.8829 (m-40) cc_final: 0.8587 (m-40) REVERT: A 1280 TRP cc_start: 0.7695 (m-10) cc_final: 0.7478 (m-10) REVERT: A 1304 ARG cc_start: 0.6616 (ttm110) cc_final: 0.6307 (ttm110) REVERT: A 1501 MET cc_start: 0.4891 (mmp) cc_final: 0.3444 (ttt) REVERT: A 1507 LYS cc_start: 0.7648 (mmmt) cc_final: 0.7442 (mttm) outliers start: 27 outliers final: 15 residues processed: 139 average time/residue: 0.2284 time to fit residues: 47.4069 Evaluate side-chains 134 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 993 ASN Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1293 HIS Chi-restraints excluded: chain A residue 1341 ASN Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1439 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 67 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 86 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 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 688 HIS A 986 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.198312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128638 restraints weight = 12715.903| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.88 r_work: 0.3156 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11610 Z= 0.172 Angle : 0.491 8.676 15738 Z= 0.253 Chirality : 0.039 0.136 1842 Planarity : 0.003 0.043 1949 Dihedral : 3.644 20.682 1541 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.97 % Allowed : 15.77 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.74 (0.23), residues: 1424 helix: 2.27 (0.17), residues: 939 sheet: -0.04 (0.66), residues: 67 loop : -1.34 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1202 HIS 0.003 0.001 HIS A 688 PHE 0.014 0.001 PHE A 851 TYR 0.013 0.001 TYR A 48 ARG 0.001 0.000 ARG A 525 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6464 (mmm) cc_final: 0.5543 (ppp) REVERT: A 63 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.6327 (t80) REVERT: A 203 ILE cc_start: 0.8171 (mm) cc_final: 0.7376 (pt) REVERT: A 500 GLU cc_start: 0.7365 (tp30) cc_final: 0.6952 (tp30) REVERT: A 634 LYS cc_start: 0.6521 (OUTLIER) cc_final: 0.6275 (ttpp) REVERT: A 688 HIS cc_start: 0.7276 (t-90) cc_final: 0.6929 (t70) REVERT: A 763 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7086 (tt0) REVERT: A 1207 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8348 (mt) REVERT: A 1276 ASN cc_start: 0.8877 (m-40) cc_final: 0.8637 (m-40) REVERT: A 1280 TRP cc_start: 0.7749 (m-10) cc_final: 0.7503 (m-10) REVERT: A 1304 ARG cc_start: 0.6646 (ttm110) cc_final: 0.6317 (ttm110) REVERT: A 1501 MET cc_start: 0.4947 (mmp) cc_final: 0.3474 (ttt) REVERT: A 1507 LYS cc_start: 0.7662 (mmmt) cc_final: 0.7462 (mttm) outliers start: 25 outliers final: 13 residues processed: 139 average time/residue: 0.2421 time to fit residues: 49.6621 Evaluate side-chains 132 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 993 ASN Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1293 HIS Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1367 HIS Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1439 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 89 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 986 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.197424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127293 restraints weight = 12620.033| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.90 r_work: 0.3139 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11610 Z= 0.193 Angle : 0.503 8.826 15738 Z= 0.259 Chirality : 0.040 0.137 1842 Planarity : 0.003 0.042 1949 Dihedral : 3.634 20.699 1541 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.89 % Allowed : 16.56 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.77 (0.23), residues: 1424 helix: 2.28 (0.17), residues: 939 sheet: 0.01 (0.66), residues: 67 loop : -1.29 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1202 HIS 0.003 0.001 HIS A1053 PHE 0.017 0.001 PHE A1236 TYR 0.020 0.001 TYR A 48 ARG 0.005 0.000 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6496 (mmm) cc_final: 0.5609 (ppp) REVERT: A 52 ARG cc_start: 0.7122 (ptp-170) cc_final: 0.6784 (ptp-170) REVERT: A 63 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.6382 (t80) REVERT: A 203 ILE cc_start: 0.8181 (mm) cc_final: 0.7384 (pt) REVERT: A 500 GLU cc_start: 0.7406 (tp30) cc_final: 0.6985 (tp30) REVERT: A 634 LYS cc_start: 0.6531 (OUTLIER) cc_final: 0.6267 (ttpp) REVERT: A 688 HIS cc_start: 0.7402 (t-90) cc_final: 0.7102 (t70) REVERT: A 763 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7119 (tt0) REVERT: A 1207 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8367 (mt) REVERT: A 1276 ASN cc_start: 0.8897 (m-40) cc_final: 0.8658 (m-40) REVERT: A 1280 TRP cc_start: 0.7811 (m-10) cc_final: 0.7526 (m-10) REVERT: A 1304 ARG cc_start: 0.6692 (ttm110) cc_final: 0.6346 (ttm110) REVERT: A 1501 MET cc_start: 0.4982 (mmp) cc_final: 0.3518 (ttt) REVERT: A 1507 LYS cc_start: 0.7685 (mmmt) cc_final: 0.7465 (mttm) outliers start: 24 outliers final: 16 residues processed: 134 average time/residue: 0.2520 time to fit residues: 50.0174 Evaluate side-chains 133 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 993 ASN Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1293 HIS Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1367 HIS Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1439 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 89 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 986 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.196972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.121869 restraints weight = 12638.844| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.80 r_work: 0.3037 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11610 Z= 0.202 Angle : 0.509 8.972 15738 Z= 0.263 Chirality : 0.040 0.144 1842 Planarity : 0.003 0.040 1949 Dihedral : 3.636 20.288 1541 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.13 % Allowed : 16.64 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.79 (0.23), residues: 1424 helix: 2.28 (0.17), residues: 939 sheet: 0.02 (0.67), residues: 67 loop : -1.26 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1202 HIS 0.003 0.001 HIS A1053 PHE 0.021 0.001 PHE A 813 TYR 0.018 0.001 TYR A 48 ARG 0.005 0.000 ARG A 914 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7113 (ptp-170) cc_final: 0.6781 (ptp-170) REVERT: A 63 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6300 (t80) REVERT: A 203 ILE cc_start: 0.8075 (mm) cc_final: 0.7237 (pt) REVERT: A 500 GLU cc_start: 0.7269 (tp30) cc_final: 0.6858 (tp30) REVERT: A 634 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.6185 (ttpp) REVERT: A 680 MET cc_start: 0.8127 (ttm) cc_final: 0.7814 (ttm) REVERT: A 688 HIS cc_start: 0.7409 (OUTLIER) cc_final: 0.7086 (t70) REVERT: A 1207 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8230 (mt) REVERT: A 1276 ASN cc_start: 0.8828 (m-40) cc_final: 0.8584 (m-40) REVERT: A 1280 TRP cc_start: 0.7768 (m-10) cc_final: 0.7482 (m-10) REVERT: A 1304 ARG cc_start: 0.6559 (ttm110) cc_final: 0.6214 (ttm110) REVERT: A 1501 MET cc_start: 0.4919 (mmp) cc_final: 0.3479 (ttt) outliers start: 27 outliers final: 17 residues processed: 133 average time/residue: 0.2585 time to fit residues: 49.8084 Evaluate side-chains 132 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 688 HIS Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 993 ASN Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1293 HIS Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1367 HIS Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1439 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 58 optimal weight: 0.1980 chunk 93 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 89 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 123 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 GLN A 986 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.198324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.123922 restraints weight = 12452.335| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.70 r_work: 0.3042 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11610 Z= 0.165 Angle : 0.501 8.875 15738 Z= 0.256 Chirality : 0.039 0.143 1842 Planarity : 0.003 0.040 1949 Dihedral : 3.565 20.090 1541 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.21 % Allowed : 16.72 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.23), residues: 1424 helix: 2.38 (0.17), residues: 943 sheet: 0.03 (0.66), residues: 67 loop : -1.27 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1202 HIS 0.002 0.001 HIS A1053 PHE 0.017 0.001 PHE A1236 TYR 0.016 0.001 TYR A 48 ARG 0.005 0.000 ARG A 914 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7139 (ptp-170) cc_final: 0.6834 (ptp-170) REVERT: A 63 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6263 (t80) REVERT: A 203 ILE cc_start: 0.8093 (mm) cc_final: 0.7248 (pt) REVERT: A 500 GLU cc_start: 0.7252 (tp30) cc_final: 0.6846 (tp30) REVERT: A 634 LYS cc_start: 0.6471 (OUTLIER) cc_final: 0.6221 (ttpp) REVERT: A 680 MET cc_start: 0.8140 (ttm) cc_final: 0.7815 (ttm) REVERT: A 797 ASN cc_start: 0.8284 (m110) cc_final: 0.7923 (m-40) REVERT: A 1207 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8223 (mt) REVERT: A 1276 ASN cc_start: 0.8836 (m-40) cc_final: 0.8597 (m-40) REVERT: A 1280 TRP cc_start: 0.7751 (m-10) cc_final: 0.7505 (m-10) REVERT: A 1304 ARG cc_start: 0.6574 (ttm110) cc_final: 0.6231 (ttm110) REVERT: A 1501 MET cc_start: 0.4918 (mmp) cc_final: 0.3477 (ttt) outliers start: 28 outliers final: 19 residues processed: 133 average time/residue: 0.2397 time to fit residues: 47.3875 Evaluate side-chains 136 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 993 ASN Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1293 HIS Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1367 HIS Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1439 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 138 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 GLN A 986 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.196528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.121872 restraints weight = 12454.735| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.71 r_work: 0.3155 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11610 Z= 0.210 Angle : 0.520 8.922 15738 Z= 0.266 Chirality : 0.040 0.143 1842 Planarity : 0.003 0.039 1949 Dihedral : 3.604 19.289 1541 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.89 % Allowed : 16.64 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.82 (0.23), residues: 1424 helix: 2.31 (0.17), residues: 939 sheet: 0.00 (0.66), residues: 67 loop : -1.24 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.003 0.001 HIS A1053 PHE 0.019 0.001 PHE A1236 TYR 0.016 0.001 TYR A 48 ARG 0.005 0.000 ARG A 914 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7291.60 seconds wall clock time: 132 minutes 54.27 seconds (7974.27 seconds total)