Starting phenix.real_space_refine on Sun Aug 4 03:09:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi3_37556/08_2024/8wi3_37556.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi3_37556/08_2024/8wi3_37556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi3_37556/08_2024/8wi3_37556.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi3_37556/08_2024/8wi3_37556.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi3_37556/08_2024/8wi3_37556.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi3_37556/08_2024/8wi3_37556.cif" } resolution = 3.38 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= 0.004 sd= 0.124 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 6099 2.51 5 N 1616 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 150": "OE1" <-> "OE2" Residue "A PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 500": "OD1" <-> "OD2" Residue "A TYR 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1043": "OD1" <-> "OD2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1077": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1152": "OE1" <-> "OE2" Residue "A ASP 1289": "OD1" <-> "OD2" Residue "A GLU 1355": "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: 9489 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 9489 Classifications: {'peptide': 1208} Link IDs: {'PTRANS': 35, 'TRANS': 1172} Chain breaks: 3 Time building chain proxies: 5.41, per 1000 atoms: 0.57 Number of scatterers: 9489 At special positions: 0 Unit cell: (77.4, 116.1, 159.96, 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 1716 8.00 N 1616 7.00 C 6099 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: 3.71 Conformation dependent library (CDL) restraints added in 1.6 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 7 sheets defined 66.1% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.689A pdb=" N ALA A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 133 removed outlier: 3.894A pdb=" N VAL A 133 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 160 removed outlier: 3.965A pdb=" N ASN A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 4.154A pdb=" N VAL A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 193 removed outlier: 3.833A pdb=" N LEU A 179 " --> pdb=" O CYS A 175 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 210 removed outlier: 4.089A pdb=" N VAL A 201 " --> pdb=" O PRO A 197 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LYS A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 263 removed outlier: 3.647A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 293 removed outlier: 4.061A pdb=" N ARG A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 removed outlier: 4.300A pdb=" N VAL A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 321 through 361 Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.813A pdb=" N TYR A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 401 removed outlier: 3.867A pdb=" N SER A 378 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 423 removed outlier: 4.279A pdb=" N ILE A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 Processing helix chain 'A' and resid 445 through 448 Processing helix chain 'A' and resid 449 through 471 removed outlier: 3.598A pdb=" N SER A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 removed outlier: 3.592A pdb=" N LEU A 609 " --> pdb=" O ILE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 645 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 663 through 670 removed outlier: 3.676A pdb=" N ALA A 668 " --> pdb=" O ARG A 664 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 669 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 702 removed outlier: 3.814A pdb=" N ASP A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 728 Processing helix chain 'A' and resid 745 through 749 removed outlier: 3.659A pdb=" N VAL A 748 " --> pdb=" O GLN A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 774 Processing helix chain 'A' and resid 775 through 786 Processing helix chain 'A' and resid 842 through 854 removed outlier: 4.427A pdb=" N TYR A 846 " --> pdb=" O PRO A 842 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 886 removed outlier: 3.857A pdb=" N PHE A 859 " --> pdb=" O GLY A 855 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 884 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 885 " --> pdb=" O SER A 881 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN A 886 " --> pdb=" O TYR A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 954 removed outlier: 3.564A pdb=" N ALA A 915 " --> pdb=" O MET A 911 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 947 " --> pdb=" O ALA A 943 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS A 948 " --> pdb=" O SER A 944 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP A 949 " --> pdb=" O SER A 945 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.946A pdb=" N ASP A 980 " --> pdb=" O SER A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1011 removed outlier: 4.139A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A1011 " --> pdb=" O ILE A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1015 removed outlier: 3.845A pdb=" N LEU A1015 " --> pdb=" O PRO A1012 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1012 through 1015' Processing helix chain 'A' and resid 1018 through 1047 removed outlier: 4.264A pdb=" N ILE A1030 " --> pdb=" O SER A1026 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL A1031 " --> pdb=" O VAL A1027 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A1042 " --> pdb=" O GLU A1038 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1059 removed outlier: 3.852A pdb=" N LEU A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1067 removed outlier: 3.871A pdb=" N ILE A1064 " --> pdb=" O GLY A1060 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A1067 " --> pdb=" O THR A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1120 Proline residue: A1087 - end of helix removed outlier: 3.711A pdb=" N MET A1120 " --> pdb=" O MET A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1138 removed outlier: 3.626A pdb=" N ALA A1129 " --> pdb=" O PRO A1125 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN A1138 " --> pdb=" O SER A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1156 removed outlier: 3.659A pdb=" N ARG A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1169 Processing helix chain 'A' and resid 1232 through 1241 removed outlier: 4.131A pdb=" N LEU A1236 " --> pdb=" O GLY A1232 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY A1237 " --> pdb=" O LYS A1233 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A1241 " --> pdb=" O GLY A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1268 Processing helix chain 'A' and resid 1284 through 1289 Processing helix chain 'A' and resid 1295 through 1306 removed outlier: 3.666A pdb=" N ILE A1299 " --> pdb=" O THR A1295 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A1306 " --> pdb=" O ALA A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1315 removed outlier: 3.504A pdb=" N ILE A1312 " --> pdb=" O MET A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1320 Processing helix chain 'A' and resid 1324 through 1328 removed outlier: 3.532A pdb=" N ASP A1328 " --> pdb=" O GLU A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1347 removed outlier: 3.916A pdb=" N ARG A1346 " --> pdb=" O ARG A1342 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS A1347 " --> pdb=" O ALA A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1376 Processing helix chain 'A' and resid 1387 through 1393 removed outlier: 3.901A pdb=" N VAL A1391 " --> pdb=" O ARG A1387 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY A1393 " --> pdb=" O HIS A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1417 Processing helix chain 'A' and resid 1420 through 1435 removed outlier: 3.559A pdb=" N LYS A1432 " --> pdb=" O ALA A1428 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL A1433 " --> pdb=" O ALA A1429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 581 through 586 removed outlier: 3.522A pdb=" N ILE A 581 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 495 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU A 583 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS A 493 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE A 585 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU A 491 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 620 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS A 493 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 618 " --> pdb=" O LYS A 493 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 575 through 576 removed outlier: 3.955A pdb=" N ALA A 498 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR A 613 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 625 through 628 removed outlier: 6.023A pdb=" N ALA A 626 " --> pdb=" O ILE A 707 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP A 709 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 628 " --> pdb=" O ASP A 709 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR A 706 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL A 740 " --> pdb=" O TYR A 706 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 708 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU A 752 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY A 765 " --> pdb=" O VAL A 753 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 755 " --> pdb=" O GLU A 763 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU A 763 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS A 757 " --> pdb=" O ILE A 761 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE A 761 " --> pdb=" O LYS A 757 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 892 through 893 Processing sheet with id=AA5, first strand: chain 'A' and resid 1216 through 1217 removed outlier: 4.371A pdb=" N ALA A1198 " --> pdb=" O GLY A1248 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY A1248 " --> pdb=" O ALA A1198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1271 through 1273 removed outlier: 3.546A pdb=" N SER A1271 " --> pdb=" O ILE A1350 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A1354 " --> pdb=" O ILE A1273 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS A1222 " --> pdb=" O ARG A1396 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N MET A1398 " --> pdb=" O LYS A1222 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY A1224 " --> pdb=" O MET A1398 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU A1400 " --> pdb=" O GLY A1224 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL A1226 " --> pdb=" O LEU A1400 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE A1397 " --> pdb=" O PHE A1408 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE A1408 " --> pdb=" O ILE A1397 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A1399 " --> pdb=" O VAL A1406 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1282 through 1283 559 hydrogen bonds defined for protein. 1632 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: 3.45 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3059 1.34 - 1.46: 2033 1.46 - 1.58: 4481 1.58 - 1.70: 1 1.70 - 1.82: 98 Bond restraints: 9672 Sorted by residual: bond pdb=" CB PRO A1277 " pdb=" CG PRO A1277 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.45e+00 bond pdb=" C ALA A 406 " pdb=" N PRO A 407 " ideal model delta sigma weight residual 1.335 1.361 -0.027 1.28e-02 6.10e+03 4.37e+00 bond pdb=" CA ALA A1086 " pdb=" C ALA A1086 " ideal model delta sigma weight residual 1.520 1.546 -0.025 1.23e-02 6.61e+03 4.22e+00 bond pdb=" C ASP A1082 " pdb=" O ASP A1082 " ideal model delta sigma weight residual 1.237 1.257 -0.021 1.17e-02 7.31e+03 3.14e+00 bond pdb=" C TRP A1097 " pdb=" O TRP A1097 " ideal model delta sigma weight residual 1.236 1.254 -0.018 1.15e-02 7.56e+03 2.49e+00 ... (remaining 9667 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.68: 218 106.68 - 113.53: 5439 113.53 - 120.38: 3727 120.38 - 127.23: 3614 127.23 - 134.08: 93 Bond angle restraints: 13091 Sorted by residual: angle pdb=" N ILE A 971 " pdb=" CA ILE A 971 " pdb=" C ILE A 971 " ideal model delta sigma weight residual 112.96 108.20 4.76 1.00e+00 1.00e+00 2.26e+01 angle pdb=" CA LEU A 956 " pdb=" CB LEU A 956 " pdb=" CG LEU A 956 " ideal model delta sigma weight residual 116.30 132.22 -15.92 3.50e+00 8.16e-02 2.07e+01 angle pdb=" C ASP A 983 " pdb=" N VAL A 984 " pdb=" CA VAL A 984 " ideal model delta sigma weight residual 123.08 118.61 4.47 1.01e+00 9.80e-01 1.96e+01 angle pdb=" CA PRO A1277 " pdb=" N PRO A1277 " pdb=" CD PRO A1277 " ideal model delta sigma weight residual 112.00 107.04 4.96 1.40e+00 5.10e-01 1.26e+01 angle pdb=" N ILE A 955 " pdb=" CA ILE A 955 " pdb=" C ILE A 955 " ideal model delta sigma weight residual 111.81 108.77 3.04 8.60e-01 1.35e+00 1.25e+01 ... (remaining 13086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4931 17.97 - 35.95: 692 35.95 - 53.92: 144 53.92 - 71.90: 27 71.90 - 89.87: 11 Dihedral angle restraints: 5805 sinusoidal: 2299 harmonic: 3506 Sorted by residual: dihedral pdb=" CA ASN A1068 " pdb=" C ASN A1068 " pdb=" N LYS A1069 " pdb=" CA LYS A1069 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA TYR A 364 " pdb=" C TYR A 364 " pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta harmonic sigma weight residual -180.00 -157.08 -22.92 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA THR A 363 " pdb=" C THR A 363 " pdb=" N TYR A 364 " pdb=" CA TYR A 364 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 5802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 992 0.032 - 0.065: 387 0.065 - 0.097: 90 0.097 - 0.129: 53 0.129 - 0.161: 10 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CA TYR A 330 " pdb=" N TYR A 330 " pdb=" C TYR A 330 " pdb=" CB TYR A 330 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CG LEU A 715 " pdb=" CB LEU A 715 " pdb=" CD1 LEU A 715 " pdb=" CD2 LEU A 715 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CB ILE A 277 " pdb=" CA ILE A 277 " pdb=" CG1 ILE A 277 " pdb=" CG2 ILE A 277 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 1529 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 664 " 0.050 5.00e-02 4.00e+02 7.50e-02 9.01e+00 pdb=" N PRO A 665 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 665 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 665 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 958 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO A 959 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 959 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 959 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 300 " 0.042 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO A 301 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " 0.036 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 586 2.73 - 3.27: 9299 3.27 - 3.81: 14563 3.81 - 4.36: 15284 4.36 - 4.90: 27669 Nonbonded interactions: 67401 Sorted by model distance: nonbonded pdb=" NZ LYS A 261 " pdb=" OE1 GLU A 475 " model vdw 2.187 3.120 nonbonded pdb=" OG1 THR A1295 " pdb=" OE1 GLN A1298 " model vdw 2.232 3.040 nonbonded pdb=" ND1 HIS A 97 " pdb=" OD1 ASN A 103 " model vdw 2.259 3.120 nonbonded pdb=" O ALA A 698 " pdb=" OG SER A 701 " model vdw 2.287 3.040 nonbonded pdb=" OG SER A 944 " pdb=" OD1 ASP A 983 " model vdw 2.320 3.040 ... (remaining 67396 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: 0.600 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.300 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 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 : 0.004 0.105 9672 Z= 0.269 Angle : 0.683 15.924 13091 Z= 0.389 Chirality : 0.040 0.161 1532 Planarity : 0.005 0.075 1640 Dihedral : 17.114 89.873 3533 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.58 % Favored : 93.33 % Rotamer: Outliers : 0.38 % Allowed : 25.10 % Favored : 74.52 % 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: 1.08 (0.25), residues: 1200 helix: 2.02 (0.19), residues: 703 sheet: 2.56 (0.67), residues: 64 loop : -1.92 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1097 HIS 0.006 0.001 HIS A 722 PHE 0.020 0.002 PHE A 434 TYR 0.019 0.002 TYR A 918 ARG 0.003 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.066 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 113 average time/residue: 0.2091 time to fit residues: 33.7579 Evaluate side-chains 113 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1205 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9672 Z= 0.215 Angle : 0.572 14.325 13091 Z= 0.306 Chirality : 0.039 0.141 1532 Planarity : 0.004 0.064 1640 Dihedral : 4.356 30.042 1304 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.17 % Favored : 93.75 % Rotamer: Outliers : 2.31 % Allowed : 23.65 % Favored : 74.04 % 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: 1.15 (0.25), residues: 1200 helix: 2.08 (0.19), residues: 716 sheet: 2.39 (0.65), residues: 69 loop : -2.04 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1097 HIS 0.004 0.001 HIS A 767 PHE 0.014 0.001 PHE A 434 TYR 0.021 0.001 TYR A 918 ARG 0.002 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 0.978 Fit side-chains REVERT: A 127 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.6822 (pm20) REVERT: A 601 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.6095 (mttt) REVERT: A 612 MET cc_start: 0.7909 (tpp) cc_final: 0.7507 (tpp) REVERT: A 674 ASP cc_start: 0.7034 (p0) cc_final: 0.6831 (p0) REVERT: A 699 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7077 (tp) REVERT: A 918 TYR cc_start: 0.6093 (OUTLIER) cc_final: 0.4978 (m-80) REVERT: A 1113 THR cc_start: 0.7468 (t) cc_final: 0.7243 (t) REVERT: A 1325 GLU cc_start: 0.8077 (pt0) cc_final: 0.7666 (pt0) REVERT: A 1360 MET cc_start: 0.1737 (OUTLIER) cc_final: 0.1486 (ppp) outliers start: 24 outliers final: 9 residues processed: 136 average time/residue: 0.1876 time to fit residues: 37.2388 Evaluate side-chains 129 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1360 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 90 optimal weight: 0.0060 chunk 74 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 117 optimal weight: 0.0000 chunk 97 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9672 Z= 0.153 Angle : 0.524 12.953 13091 Z= 0.274 Chirality : 0.038 0.139 1532 Planarity : 0.004 0.061 1640 Dihedral : 4.154 26.003 1303 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.83 % Favored : 94.00 % Rotamer: Outliers : 2.60 % Allowed : 25.38 % Favored : 72.02 % 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: 1.44 (0.25), residues: 1200 helix: 2.29 (0.19), residues: 724 sheet: 2.39 (0.64), residues: 69 loop : -1.95 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1097 HIS 0.007 0.001 HIS A 722 PHE 0.009 0.001 PHE A1088 TYR 0.011 0.001 TYR A 918 ARG 0.003 0.000 ARG A 690 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 0.963 Fit side-chains REVERT: A 320 PHE cc_start: 0.6404 (OUTLIER) cc_final: 0.5890 (t80) REVERT: A 601 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.5851 (mttt) REVERT: A 949 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.6528 (t0) REVERT: A 960 MET cc_start: 0.5137 (pmm) cc_final: 0.4807 (tpt) REVERT: A 1308 MET cc_start: 0.6730 (mmm) cc_final: 0.6360 (tpt) REVERT: A 1360 MET cc_start: 0.1735 (OUTLIER) cc_final: 0.1446 (ppp) REVERT: A 1425 MET cc_start: 0.3682 (mmp) cc_final: 0.3434 (mmp) outliers start: 27 outliers final: 10 residues processed: 143 average time/residue: 0.1869 time to fit residues: 38.6512 Evaluate side-chains 130 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1360 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 HIS A1298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9672 Z= 0.196 Angle : 0.534 10.746 13091 Z= 0.280 Chirality : 0.039 0.144 1532 Planarity : 0.004 0.079 1640 Dihedral : 3.958 25.650 1300 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.17 % Favored : 93.75 % Rotamer: Outliers : 3.37 % Allowed : 24.33 % Favored : 72.31 % 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: 1.41 (0.25), residues: 1200 helix: 2.26 (0.19), residues: 725 sheet: 2.43 (0.64), residues: 69 loop : -1.97 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1097 HIS 0.014 0.001 HIS A 722 PHE 0.015 0.001 PHE A 434 TYR 0.019 0.001 TYR A 918 ARG 0.002 0.000 ARG A 974 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 121 time to evaluate : 1.041 Fit side-chains REVERT: A 320 PHE cc_start: 0.6569 (OUTLIER) cc_final: 0.6091 (t80) REVERT: A 601 LYS cc_start: 0.6385 (OUTLIER) cc_final: 0.5920 (mttt) REVERT: A 918 TYR cc_start: 0.5759 (OUTLIER) cc_final: 0.4637 (m-80) REVERT: A 949 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.6608 (t0) REVERT: A 960 MET cc_start: 0.5253 (pmm) cc_final: 0.4953 (tpt) REVERT: A 1360 MET cc_start: 0.1679 (OUTLIER) cc_final: 0.1445 (ppp) REVERT: A 1398 MET cc_start: 0.5407 (tpp) cc_final: 0.3829 (ttm) REVERT: A 1425 MET cc_start: 0.3556 (mmp) cc_final: 0.3355 (mmp) outliers start: 35 outliers final: 17 residues processed: 143 average time/residue: 0.1861 time to fit residues: 39.7867 Evaluate side-chains 140 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1360 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 59 optimal weight: 30.0000 chunk 104 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9672 Z= 0.204 Angle : 0.556 14.769 13091 Z= 0.289 Chirality : 0.039 0.211 1532 Planarity : 0.004 0.067 1640 Dihedral : 3.992 25.397 1300 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.50 % Favored : 93.42 % Rotamer: Outliers : 3.65 % Allowed : 24.62 % Favored : 71.73 % 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: 1.36 (0.25), residues: 1200 helix: 2.22 (0.19), residues: 724 sheet: 2.60 (0.65), residues: 64 loop : -1.97 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1097 HIS 0.020 0.001 HIS A 722 PHE 0.015 0.001 PHE A 434 TYR 0.018 0.001 TYR A 918 ARG 0.002 0.000 ARG A1335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 121 time to evaluate : 0.983 Fit side-chains REVERT: A 127 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.6780 (pm20) REVERT: A 320 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.6142 (t80) REVERT: A 601 LYS cc_start: 0.6464 (OUTLIER) cc_final: 0.5943 (mttt) REVERT: A 674 ASP cc_start: 0.7186 (p0) cc_final: 0.6948 (p0) REVERT: A 907 ASP cc_start: 0.8169 (t0) cc_final: 0.7749 (t0) REVERT: A 918 TYR cc_start: 0.6075 (OUTLIER) cc_final: 0.4907 (m-80) REVERT: A 949 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.6670 (t0) REVERT: A 960 MET cc_start: 0.5238 (pmm) cc_final: 0.4921 (tpt) REVERT: A 979 MET cc_start: 0.8396 (mmm) cc_final: 0.7806 (mmp) REVERT: A 1360 MET cc_start: 0.1345 (OUTLIER) cc_final: 0.1122 (ppp) REVERT: A 1398 MET cc_start: 0.5565 (tpp) cc_final: 0.3793 (ttm) outliers start: 38 outliers final: 27 residues processed: 147 average time/residue: 0.1822 time to fit residues: 40.0412 Evaluate side-chains 152 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1283 THR Chi-restraints excluded: chain A residue 1360 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 7.9990 chunk 104 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 0.1980 chunk 96 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 30.0000 chunk 60 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9672 Z= 0.198 Angle : 0.550 9.351 13091 Z= 0.286 Chirality : 0.039 0.220 1532 Planarity : 0.004 0.062 1640 Dihedral : 3.991 25.496 1300 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.42 % Favored : 93.50 % Rotamer: Outliers : 4.04 % Allowed : 24.13 % Favored : 71.83 % 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: 1.38 (0.25), residues: 1200 helix: 2.22 (0.19), residues: 724 sheet: 2.73 (0.64), residues: 63 loop : -1.92 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1097 HIS 0.020 0.001 HIS A 722 PHE 0.014 0.001 PHE A 434 TYR 0.018 0.001 TYR A 918 ARG 0.003 0.000 ARG A1335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 121 time to evaluate : 1.049 Fit side-chains REVERT: A 127 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: A 320 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.6163 (t80) REVERT: A 478 MET cc_start: 0.5275 (tpp) cc_final: 0.4324 (ttt) REVERT: A 601 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.5983 (mttt) REVERT: A 907 ASP cc_start: 0.8202 (t0) cc_final: 0.7786 (t0) REVERT: A 918 TYR cc_start: 0.6151 (OUTLIER) cc_final: 0.4922 (m-80) REVERT: A 949 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.6676 (t0) REVERT: A 960 MET cc_start: 0.5296 (pmm) cc_final: 0.4947 (tpt) REVERT: A 1360 MET cc_start: 0.1655 (OUTLIER) cc_final: 0.1425 (ppp) REVERT: A 1398 MET cc_start: 0.5610 (tpp) cc_final: 0.3780 (ttp) outliers start: 42 outliers final: 27 residues processed: 149 average time/residue: 0.1808 time to fit residues: 39.8363 Evaluate side-chains 152 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1283 THR Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1360 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9672 Z= 0.205 Angle : 0.555 9.151 13091 Z= 0.292 Chirality : 0.039 0.193 1532 Planarity : 0.004 0.061 1640 Dihedral : 4.004 25.377 1300 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.42 % Favored : 93.50 % Rotamer: Outliers : 4.52 % Allowed : 23.75 % Favored : 71.73 % 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: 1.35 (0.25), residues: 1200 helix: 2.20 (0.19), residues: 724 sheet: 2.69 (0.65), residues: 64 loop : -1.97 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1097 HIS 0.020 0.001 HIS A 722 PHE 0.015 0.001 PHE A 434 TYR 0.019 0.001 TYR A 918 ARG 0.002 0.000 ARG A 974 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 120 time to evaluate : 0.944 Fit side-chains REVERT: A 127 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.6773 (pm20) REVERT: A 320 PHE cc_start: 0.6656 (OUTLIER) cc_final: 0.6183 (t80) REVERT: A 601 LYS cc_start: 0.6557 (OUTLIER) cc_final: 0.6007 (mttt) REVERT: A 907 ASP cc_start: 0.8231 (t0) cc_final: 0.7901 (t0) REVERT: A 918 TYR cc_start: 0.6213 (OUTLIER) cc_final: 0.4985 (m-80) REVERT: A 949 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.6674 (t0) REVERT: A 960 MET cc_start: 0.5381 (pmm) cc_final: 0.4967 (tpt) REVERT: A 1360 MET cc_start: 0.1604 (OUTLIER) cc_final: 0.1337 (ppp) REVERT: A 1398 MET cc_start: 0.5677 (tpp) cc_final: 0.3873 (ttp) outliers start: 47 outliers final: 32 residues processed: 154 average time/residue: 0.1733 time to fit residues: 39.5694 Evaluate side-chains 156 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 118 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1283 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1360 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS ** A 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9672 Z= 0.184 Angle : 0.546 9.028 13091 Z= 0.286 Chirality : 0.039 0.170 1532 Planarity : 0.004 0.061 1640 Dihedral : 3.985 25.485 1300 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.67 % Favored : 93.25 % Rotamer: Outliers : 3.46 % Allowed : 25.48 % Favored : 71.06 % 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: 1.43 (0.25), residues: 1200 helix: 2.25 (0.19), residues: 724 sheet: 2.82 (0.65), residues: 63 loop : -1.90 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1097 HIS 0.021 0.001 HIS A 722 PHE 0.012 0.001 PHE A 434 TYR 0.017 0.001 TYR A 918 ARG 0.003 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 0.919 Fit side-chains REVERT: A 127 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: A 320 PHE cc_start: 0.6642 (OUTLIER) cc_final: 0.6147 (t80) REVERT: A 601 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6015 (mttt) REVERT: A 907 ASP cc_start: 0.8229 (t0) cc_final: 0.7910 (t0) REVERT: A 918 TYR cc_start: 0.6040 (OUTLIER) cc_final: 0.4853 (m-80) REVERT: A 949 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.6692 (t0) REVERT: A 960 MET cc_start: 0.5300 (pmm) cc_final: 0.4941 (tpt) REVERT: A 974 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.5832 (ttp-110) REVERT: A 1360 MET cc_start: 0.1333 (OUTLIER) cc_final: 0.0977 (ppp) REVERT: A 1398 MET cc_start: 0.5723 (tpp) cc_final: 0.5296 (mmt) outliers start: 36 outliers final: 26 residues processed: 143 average time/residue: 0.1842 time to fit residues: 38.6799 Evaluate side-chains 149 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 974 ARG Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1360 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 10.0000 chunk 101 optimal weight: 0.0060 chunk 107 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9672 Z= 0.211 Angle : 0.566 12.477 13091 Z= 0.296 Chirality : 0.039 0.164 1532 Planarity : 0.004 0.061 1640 Dihedral : 3.992 25.498 1300 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.50 % Favored : 93.33 % Rotamer: Outliers : 4.42 % Allowed : 24.62 % Favored : 70.96 % 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: 1.35 (0.25), residues: 1200 helix: 2.18 (0.19), residues: 724 sheet: 2.82 (0.66), residues: 63 loop : -1.92 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1097 HIS 0.022 0.001 HIS A 722 PHE 0.015 0.001 PHE A 434 TYR 0.020 0.001 TYR A 918 ARG 0.002 0.000 ARG A 974 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 122 time to evaluate : 1.036 Fit side-chains REVERT: A 127 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.6778 (pm20) REVERT: A 320 PHE cc_start: 0.6624 (OUTLIER) cc_final: 0.6164 (t80) REVERT: A 478 MET cc_start: 0.5327 (tpp) cc_final: 0.4417 (ttt) REVERT: A 907 ASP cc_start: 0.8267 (t0) cc_final: 0.7954 (t0) REVERT: A 918 TYR cc_start: 0.6260 (OUTLIER) cc_final: 0.5144 (m-80) REVERT: A 949 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.6699 (t0) REVERT: A 974 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.5877 (ttp-110) REVERT: A 979 MET cc_start: 0.8330 (mmm) cc_final: 0.7748 (mmp) REVERT: A 1154 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6633 (tp30) REVERT: A 1360 MET cc_start: 0.1603 (OUTLIER) cc_final: 0.1291 (ppp) REVERT: A 1398 MET cc_start: 0.5779 (tpp) cc_final: 0.5333 (mmt) outliers start: 46 outliers final: 32 residues processed: 154 average time/residue: 0.1753 time to fit residues: 40.0785 Evaluate side-chains 158 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 119 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 974 ARG Chi-restraints excluded: chain A residue 996 ASN Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1154 GLU Chi-restraints excluded: chain A residue 1159 SER Chi-restraints excluded: chain A residue 1166 TYR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1324 MET Chi-restraints excluded: chain A residue 1360 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 95 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 75 optimal weight: 0.0170 chunk 101 optimal weight: 0.0370 chunk 29 optimal weight: 0.9980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9672 Z= 0.160 Angle : 0.542 8.536 13091 Z= 0.281 Chirality : 0.039 0.154 1532 Planarity : 0.004 0.062 1640 Dihedral : 3.969 25.712 1300 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.08 % Favored : 93.75 % Rotamer: Outliers : 2.69 % Allowed : 26.15 % Favored : 71.15 % 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: 1.56 (0.25), residues: 1200 helix: 2.37 (0.19), residues: 724 sheet: 2.94 (0.66), residues: 63 loop : -1.90 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1097 HIS 0.022 0.001 HIS A 722 PHE 0.009 0.001 PHE A 194 TYR 0.014 0.001 TYR A 700 ARG 0.002 0.000 ARG A 974 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 1.047 Fit side-chains REVERT: A 127 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.6654 (pm20) REVERT: A 320 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.6167 (t80) REVERT: A 612 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7281 (ttp) REVERT: A 907 ASP cc_start: 0.8195 (t0) cc_final: 0.7878 (t0) REVERT: A 918 TYR cc_start: 0.5614 (OUTLIER) cc_final: 0.4525 (m-80) REVERT: A 970 ARG cc_start: 0.7582 (ptp90) cc_final: 0.6465 (mtp180) REVERT: A 974 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6245 (ttp-110) REVERT: A 1116 MET cc_start: 0.5074 (tpt) cc_final: 0.4648 (tpt) REVERT: A 1154 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6614 (tp30) REVERT: A 1398 MET cc_start: 0.5785 (tpp) cc_final: 0.5363 (mmt) outliers start: 28 outliers final: 15 residues processed: 142 average time/residue: 0.1825 time to fit residues: 38.2783 Evaluate side-chains 141 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 918 TYR Chi-restraints excluded: chain A residue 974 ARG Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1154 GLU Chi-restraints excluded: chain A residue 1272 ILE Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1324 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 39 optimal weight: 0.0050 chunk 97 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 722 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.240612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.208004 restraints weight = 10797.805| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 1.77 r_work: 0.4065 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9672 Z= 0.165 Angle : 0.544 12.988 13091 Z= 0.279 Chirality : 0.039 0.149 1532 Planarity : 0.004 0.076 1640 Dihedral : 3.932 26.109 1300 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.67 % Favored : 93.25 % Rotamer: Outliers : 2.50 % Allowed : 26.44 % Favored : 71.06 % 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: 1.56 (0.25), residues: 1200 helix: 2.39 (0.19), residues: 726 sheet: 3.21 (0.69), residues: 58 loop : -1.95 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1097 HIS 0.022 0.001 HIS A 722 PHE 0.010 0.001 PHE A 434 TYR 0.015 0.001 TYR A 918 ARG 0.002 0.000 ARG A 974 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.28 seconds wall clock time: 33 minutes 59.61 seconds (2039.61 seconds total)