Starting phenix.real_space_refine on Mon Mar 11 17:36:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1n_33567/03_2024/7y1n_33567_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1n_33567/03_2024/7y1n_33567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1n_33567/03_2024/7y1n_33567.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1n_33567/03_2024/7y1n_33567.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1n_33567/03_2024/7y1n_33567_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1n_33567/03_2024/7y1n_33567_updated.pdb" } resolution = 3.61 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= 0.005 sd= 0.079 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 39 5.16 5 C 5712 2.51 5 N 1467 2.21 5 O 1538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8763 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 8763 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'BJX': 1} Classifications: {'peptide': 1171, 'undetermined': 5} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 35, 'TRANS': 1135, None: 5} Not linked: pdbres="MET A1545 " pdbres="ADP A3001 " Not linked: pdbres="ADP A3001 " pdbres=" MG A3002 " Not linked: pdbres=" MG A3002 " pdbres=" MG A3003 " Not linked: pdbres=" MG A3003 " pdbres="ATP A3004 " Not linked: pdbres="ATP A3004 " pdbres="BJX A3005 " Chain breaks: 7 Unresolved non-hydrogen bonds: 571 Unresolved non-hydrogen angles: 701 Unresolved non-hydrogen dihedrals: 455 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 34, 'GLU:plan': 27, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 352 Time building chain proxies: 5.33, per 1000 atoms: 0.61 Number of scatterers: 8763 At special positions: 0 Unit cell: (69.222, 95.076, 133.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 5 15.00 Mg 2 11.99 O 1538 8.00 N 1467 7.00 C 5712 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: 3.82 Conformation dependent library (CDL) restraints added in 1.9 seconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 6 sheets defined 66.3% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 229 through 236 removed outlier: 5.184A pdb=" N THR A 233 " --> pdb=" O TRP A 230 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE A 236 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 274 Processing helix chain 'A' and resid 285 through 324 removed outlier: 6.473A pdb=" N ARG A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix removed outlier: 3.819A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 343 through 346 No H-bonds generated for 'chain 'A' and resid 343 through 346' Processing helix chain 'A' and resid 348 through 393 Processing helix chain 'A' and resid 406 through 497 removed outlier: 3.628A pdb=" N GLU A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N THR A 418 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Proline residue: A 429 - end of helix removed outlier: 3.798A pdb=" N TRP A 432 " --> pdb=" O CYS A 428 " (cutoff:3.500A) Proline residue: A 435 - end of helix removed outlier: 8.338A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N SER A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 499 through 505 Processing helix chain 'A' and resid 508 through 558 Proline residue: A 544 - end of helix Processing helix chain 'A' and resid 565 through 607 removed outlier: 4.290A pdb=" N THR A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) Proline residue: A 581 - end of helix removed outlier: 4.080A pdb=" N SER A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 607 " --> pdb=" O ASN A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 removed outlier: 3.680A pdb=" N LEU A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 767 Processing helix chain 'A' and resid 774 through 784 Processing helix chain 'A' and resid 787 through 792 removed outlier: 3.627A pdb=" N ASP A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 823 Processing helix chain 'A' and resid 840 through 849 removed outlier: 3.509A pdb=" N GLU A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 869 through 874 removed outlier: 4.140A pdb=" N THR A 873 " --> pdb=" O GLN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 898 Processing helix chain 'A' and resid 900 through 910 Processing helix chain 'A' and resid 975 through 985 removed outlier: 4.227A pdb=" N GLY A 985 " --> pdb=" O TYR A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1016 Processing helix chain 'A' and resid 1029 through 1074 removed outlier: 3.807A pdb=" N ASN A1067 " --> pdb=" O ASN A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1082 Processing helix chain 'A' and resid 1085 through 1127 removed outlier: 3.803A pdb=" N PHE A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP A1095 " --> pdb=" O ARG A1091 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE A1103 " --> pdb=" O ILE A1099 " (cutoff:3.500A) Proline residue: A1104 - end of helix Processing helix chain 'A' and resid 1129 through 1175 removed outlier: 3.671A pdb=" N ALA A1136 " --> pdb=" O ILE A1133 " (cutoff:3.500A) Proline residue: A1137 - end of helix removed outlier: 3.538A pdb=" N ARG A1150 " --> pdb=" O LYS A1147 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER A1153 " --> pdb=" O ARG A1150 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A1165 " --> pdb=" O SER A1162 " (cutoff:3.500A) Proline residue: A1166 - end of helix removed outlier: 3.533A pdb=" N ALA A1175 " --> pdb=" O SER A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1184 Processing helix chain 'A' and resid 1187 through 1235 removed outlier: 3.666A pdb=" N THR A1200 " --> pdb=" O GLU A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1282 removed outlier: 3.639A pdb=" N THR A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TRP A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1304 No H-bonds generated for 'chain 'A' and resid 1302 through 1304' Processing helix chain 'A' and resid 1348 through 1356 removed outlier: 4.098A pdb=" N PHE A1355 " --> pdb=" O LEU A1351 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE A1356 " --> pdb=" O SER A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1375 No H-bonds generated for 'chain 'A' and resid 1373 through 1375' Processing helix chain 'A' and resid 1378 through 1383 Processing helix chain 'A' and resid 1399 through 1403 Processing helix chain 'A' and resid 1411 through 1421 Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1440 through 1442 No H-bonds generated for 'chain 'A' and resid 1440 through 1442' Processing helix chain 'A' and resid 1447 through 1461 removed outlier: 4.001A pdb=" N ARG A1461 " --> pdb=" O ARG A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1490 Processing helix chain 'A' and resid 1503 through 1506 Processing helix chain 'A' and resid 1526 through 1531 Processing helix chain 'A' and resid 1536 through 1544 Processing sheet with id= A, first strand: chain 'A' and resid 725 through 727 removed outlier: 6.753A pdb=" N ILE A 691 " --> pdb=" O ALA A 667 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 885 through 890 removed outlier: 6.445A pdb=" N ALA A 880 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A 889 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 878 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL A 862 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE A 699 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU A 864 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N GLY A 701 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1308 through 1311 Processing sheet with id= D, first strand: chain 'A' and resid 1520 through 1524 removed outlier: 6.913A pdb=" N VAL A1514 " --> pdb=" O LEU A1521 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR A1523 " --> pdb=" O VAL A1512 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A1512 " --> pdb=" O TYR A1523 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL A1496 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE A1340 " --> pdb=" O VAL A1496 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR A1498 " --> pdb=" O ILE A1340 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N GLY A1342 " --> pdb=" O THR A1498 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER A1386 " --> pdb=" O ILE A1467 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASP A1469 " --> pdb=" O SER A1386 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A1388 " --> pdb=" O ASP A1469 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 684 through 687 removed outlier: 5.676A pdb=" N GLY A 673 " --> pdb=" O ASN A 686 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER A 676 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR A 720 " --> pdb=" O SER A 676 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1313 through 1315 removed outlier: 7.947A pdb=" N VAL A1315 " --> pdb=" O LYS A1326 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS A1326 " --> pdb=" O VAL A1315 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1611 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1331 1.31 - 1.43: 2415 1.43 - 1.56: 5119 1.56 - 1.68: 15 1.68 - 1.81: 65 Bond restraints: 8945 Sorted by residual: bond pdb=" C4 ATP A3004 " pdb=" C5 ATP A3004 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.85e+01 bond pdb=" C16 BJX A3005 " pdb=" N1 BJX A3005 " ideal model delta sigma weight residual 1.344 1.457 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C5 ATP A3004 " pdb=" C6 ATP A3004 " ideal model delta sigma weight residual 1.409 1.464 -0.055 1.00e-02 1.00e+04 3.03e+01 bond pdb=" C5 ATP A3004 " pdb=" N7 ATP A3004 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.89e+01 bond pdb=" CA TYR A1031 " pdb=" C TYR A1031 " ideal model delta sigma weight residual 1.523 1.591 -0.068 1.30e-02 5.92e+03 2.74e+01 ... (remaining 8940 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.48: 219 106.48 - 113.88: 5314 113.88 - 121.29: 4769 121.29 - 128.70: 1838 128.70 - 136.10: 76 Bond angle restraints: 12216 Sorted by residual: angle pdb=" PB ATP A3004 " pdb=" O3B ATP A3004 " pdb=" PG ATP A3004 " ideal model delta sigma weight residual 139.87 116.43 23.44 1.00e+00 1.00e+00 5.49e+02 angle pdb=" PA ATP A3004 " pdb=" O3A ATP A3004 " pdb=" PB ATP A3004 " ideal model delta sigma weight residual 136.83 115.68 21.15 1.00e+00 1.00e+00 4.47e+02 angle pdb=" C5 ATP A3004 " pdb=" C4 ATP A3004 " pdb=" N3 ATP A3004 " ideal model delta sigma weight residual 126.80 118.33 8.47 1.00e+00 1.00e+00 7.17e+01 angle pdb=" N3 ATP A3004 " pdb=" C4 ATP A3004 " pdb=" N9 ATP A3004 " ideal model delta sigma weight residual 127.04 136.10 -9.06 1.15e+00 7.59e-01 6.23e+01 angle pdb=" C ASN A 399 " pdb=" N LEU A 400 " pdb=" CA LEU A 400 " ideal model delta sigma weight residual 120.28 111.24 9.04 1.34e+00 5.57e-01 4.55e+01 ... (remaining 12211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.12: 5181 32.12 - 64.24: 65 64.24 - 96.36: 6 96.36 - 128.48: 2 128.48 - 160.60: 2 Dihedral angle restraints: 5256 sinusoidal: 1846 harmonic: 3410 Sorted by residual: dihedral pdb=" O1B ADP A3001 " pdb=" O3A ADP A3001 " pdb=" PB ADP A3001 " pdb=" PA ADP A3001 " ideal model delta sinusoidal sigma weight residual 300.00 142.89 157.11 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C5' ADP A3001 " pdb=" O5' ADP A3001 " pdb=" PA ADP A3001 " pdb=" O2A ADP A3001 " ideal model delta sinusoidal sigma weight residual -60.00 -158.59 98.59 1 2.00e+01 2.50e-03 2.76e+01 dihedral pdb=" O2A ADP A3001 " pdb=" O3A ADP A3001 " pdb=" PA ADP A3001 " pdb=" PB ADP A3001 " ideal model delta sinusoidal sigma weight residual -60.00 -144.53 84.53 1 2.00e+01 2.50e-03 2.17e+01 ... (remaining 5253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1262 0.050 - 0.100: 186 0.100 - 0.150: 42 0.150 - 0.200: 2 0.200 - 0.251: 5 Chirality restraints: 1497 Sorted by residual: chirality pdb=" C1' ATP A3004 " pdb=" C2' ATP A3004 " pdb=" N9 ATP A3004 " pdb=" O4' ATP A3004 " both_signs ideal model delta sigma weight residual False 2.41 2.66 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ASN A 399 " pdb=" N ASN A 399 " pdb=" C ASN A 399 " pdb=" CB ASN A 399 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA VAL A 703 " pdb=" N VAL A 703 " pdb=" C VAL A 703 " pdb=" CB VAL A 703 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1494 not shown) Planarity restraints: 1487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 399 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.06e+00 pdb=" C ASN A 399 " 0.035 2.00e-02 2.50e+03 pdb=" O ASN A 399 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 400 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 707 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C LYS A 707 " -0.032 2.00e-02 2.50e+03 pdb=" O LYS A 707 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 708 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1376 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A1377 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A1377 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1377 " -0.025 5.00e-02 4.00e+02 ... (remaining 1484 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 141 2.67 - 3.23: 9446 3.23 - 3.79: 14199 3.79 - 4.34: 17554 4.34 - 4.90: 30163 Nonbonded interactions: 71503 Sorted by model distance: nonbonded pdb=" N GLU A 508 " pdb=" OE1 GLU A 508 " model vdw 2.118 2.520 nonbonded pdb=" O ASN A 399 " pdb=" OD1 ASN A 399 " model vdw 2.153 3.040 nonbonded pdb=" O1A ADP A3001 " pdb=" O3B ADP A3001 " model vdw 2.153 3.040 nonbonded pdb=" O2B ATP A3004 " pdb=" O2G ATP A3004 " model vdw 2.161 3.040 nonbonded pdb="MG MG A3003 " pdb=" O3G ATP A3004 " model vdw 2.194 2.170 ... (remaining 71498 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 7.150 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.950 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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 : 0.005 0.113 8945 Z= 0.342 Angle : 0.700 23.438 12216 Z= 0.471 Chirality : 0.040 0.251 1497 Planarity : 0.003 0.044 1487 Dihedral : 12.084 160.597 3044 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.30 % Allowed : 3.42 % Favored : 95.28 % 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: 2.40 (0.25), residues: 1155 helix: 2.35 (0.18), residues: 789 sheet: 0.73 (0.75), residues: 50 loop : -0.21 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1214 HIS 0.005 0.001 HIS A1001 PHE 0.008 0.001 PHE A 552 TYR 0.020 0.001 TYR A1031 ARG 0.003 0.000 ARG A1185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 LEU cc_start: 0.8555 (tp) cc_final: 0.8344 (tp) REVERT: A 355 LEU cc_start: 0.9257 (tp) cc_final: 0.9045 (tp) REVERT: A 425 LEU cc_start: 0.9062 (tp) cc_final: 0.8825 (tp) REVERT: A 525 SER cc_start: 0.9181 (m) cc_final: 0.8980 (t) REVERT: A 717 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7965 (mm-30) REVERT: A 719 GLN cc_start: 0.8225 (mt0) cc_final: 0.7917 (mt0) REVERT: A 750 TYR cc_start: 0.9126 (t80) cc_final: 0.8636 (t80) REVERT: A 1011 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9216 (tt) REVERT: A 1173 GLU cc_start: 0.7887 (pt0) cc_final: 0.7686 (pt0) REVERT: A 1426 MET cc_start: 0.7743 (tmm) cc_final: 0.7339 (tmm) outliers start: 11 outliers final: 5 residues processed: 162 average time/residue: 0.1944 time to fit residues: 44.7852 Evaluate side-chains 119 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1185 ARG Chi-restraints excluded: chain A residue 1427 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8945 Z= 0.253 Angle : 0.599 6.862 12216 Z= 0.296 Chirality : 0.041 0.147 1497 Planarity : 0.004 0.042 1487 Dihedral : 10.965 161.031 1316 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.13 % Allowed : 10.15 % Favored : 87.72 % 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: 2.54 (0.25), residues: 1155 helix: 2.43 (0.18), residues: 791 sheet: 0.78 (0.75), residues: 50 loop : -0.09 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1260 HIS 0.005 0.001 HIS A1065 PHE 0.013 0.002 PHE A 835 TYR 0.010 0.001 TYR A 750 ARG 0.006 0.001 ARG A1213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.6888 (mm) REVERT: A 345 LEU cc_start: 0.8319 (tt) cc_final: 0.8083 (tp) REVERT: A 355 LEU cc_start: 0.9215 (tp) cc_final: 0.8990 (tp) REVERT: A 717 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7999 (mm-30) REVERT: A 750 TYR cc_start: 0.9119 (t80) cc_final: 0.8725 (t80) REVERT: A 832 ASP cc_start: 0.8634 (t0) cc_final: 0.8245 (m-30) REVERT: A 1011 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9265 (tt) REVERT: A 1426 MET cc_start: 0.7757 (tmm) cc_final: 0.7258 (tmm) outliers start: 18 outliers final: 14 residues processed: 145 average time/residue: 0.1630 time to fit residues: 35.3906 Evaluate side-chains 123 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1472 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 105 optimal weight: 0.0470 chunk 36 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- 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: 0.8258 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8945 Z= 0.170 Angle : 0.544 9.510 12216 Z= 0.267 Chirality : 0.040 0.172 1497 Planarity : 0.004 0.044 1487 Dihedral : 10.039 164.328 1311 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.72 % Allowed : 10.74 % Favored : 86.54 % 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: 2.58 (0.25), residues: 1155 helix: 2.45 (0.18), residues: 791 sheet: 0.73 (0.73), residues: 50 loop : -0.04 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 756 HIS 0.004 0.001 HIS A1065 PHE 0.013 0.001 PHE A 835 TYR 0.008 0.001 TYR A 750 ARG 0.005 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 355 LEU cc_start: 0.9187 (tp) cc_final: 0.8979 (tp) REVERT: A 428 CYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7582 (t) REVERT: A 717 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7917 (mm-30) REVERT: A 719 GLN cc_start: 0.8272 (mt0) cc_final: 0.7916 (mt0) REVERT: A 750 TYR cc_start: 0.9101 (t80) cc_final: 0.8772 (t80) REVERT: A 1011 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9212 (tt) REVERT: A 1030 PHE cc_start: 0.8711 (t80) cc_final: 0.8379 (t80) REVERT: A 1403 LEU cc_start: 0.8975 (mm) cc_final: 0.8750 (mt) REVERT: A 1426 MET cc_start: 0.7801 (tmm) cc_final: 0.7290 (tmm) REVERT: A 1496 VAL cc_start: 0.8906 (m) cc_final: 0.8595 (t) outliers start: 23 outliers final: 16 residues processed: 143 average time/residue: 0.1566 time to fit residues: 34.3358 Evaluate side-chains 125 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1472 THR Chi-restraints excluded: chain A residue 1498 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.0370 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 overall best weight: 1.4860 ------------------------------------------------------------------------------- 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: 0.8317 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8945 Z= 0.272 Angle : 0.583 8.932 12216 Z= 0.286 Chirality : 0.041 0.163 1497 Planarity : 0.004 0.049 1487 Dihedral : 9.616 164.715 1311 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.66 % Allowed : 12.63 % Favored : 83.71 % 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: 2.40 (0.25), residues: 1155 helix: 2.32 (0.18), residues: 791 sheet: 0.65 (0.72), residues: 50 loop : -0.11 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1214 HIS 0.005 0.001 HIS A1065 PHE 0.011 0.001 PHE A 312 TYR 0.013 0.001 TYR A 484 ARG 0.005 0.000 ARG A1213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.6941 (mm) REVERT: A 355 LEU cc_start: 0.9198 (tp) cc_final: 0.8984 (tp) REVERT: A 717 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7893 (mm-30) REVERT: A 719 GLN cc_start: 0.8292 (mt0) cc_final: 0.7910 (mt0) REVERT: A 750 TYR cc_start: 0.9161 (t80) cc_final: 0.8811 (t80) REVERT: A 1011 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9147 (tt) REVERT: A 1030 PHE cc_start: 0.8698 (t80) cc_final: 0.8394 (t80) REVERT: A 1496 VAL cc_start: 0.8873 (m) cc_final: 0.8563 (t) outliers start: 31 outliers final: 20 residues processed: 142 average time/residue: 0.1589 time to fit residues: 34.6777 Evaluate side-chains 127 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1472 THR Chi-restraints excluded: chain A residue 1498 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8288 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8945 Z= 0.217 Angle : 0.548 6.785 12216 Z= 0.269 Chirality : 0.040 0.199 1497 Planarity : 0.004 0.052 1487 Dihedral : 9.044 165.061 1310 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 3.54 % Allowed : 13.70 % Favored : 82.76 % 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: 2.40 (0.25), residues: 1155 helix: 2.32 (0.19), residues: 792 sheet: 0.44 (0.66), residues: 65 loop : -0.11 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1214 HIS 0.005 0.001 HIS A1065 PHE 0.017 0.001 PHE A 991 TYR 0.009 0.001 TYR A 777 ARG 0.004 0.000 ARG A 804 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.6766 (mm) REVERT: A 355 LEU cc_start: 0.9176 (tp) cc_final: 0.8971 (tp) REVERT: A 432 TRP cc_start: 0.7896 (m-90) cc_final: 0.6770 (m100) REVERT: A 710 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9152 (tt) REVERT: A 717 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7887 (mm-30) REVERT: A 719 GLN cc_start: 0.8301 (mt0) cc_final: 0.7934 (mt0) REVERT: A 750 TYR cc_start: 0.9137 (t80) cc_final: 0.8837 (t80) REVERT: A 1011 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9090 (tt) REVERT: A 1030 PHE cc_start: 0.8598 (t80) cc_final: 0.8273 (t80) outliers start: 30 outliers final: 21 residues processed: 138 average time/residue: 0.1679 time to fit residues: 35.1200 Evaluate side-chains 129 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1308 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1472 THR Chi-restraints excluded: chain A residue 1498 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 40.0000 chunk 109 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.8273 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8945 Z= 0.195 Angle : 0.537 6.946 12216 Z= 0.262 Chirality : 0.039 0.215 1497 Planarity : 0.004 0.052 1487 Dihedral : 8.665 163.259 1310 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.54 % Allowed : 14.40 % Favored : 82.05 % 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: 2.46 (0.25), residues: 1155 helix: 2.37 (0.19), residues: 792 sheet: 0.62 (0.68), residues: 60 loop : -0.14 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1214 HIS 0.005 0.001 HIS A1065 PHE 0.019 0.001 PHE A 991 TYR 0.008 0.001 TYR A 777 ARG 0.003 0.000 ARG A 804 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 297 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.6669 (mm) REVERT: A 425 LEU cc_start: 0.8917 (tp) cc_final: 0.8662 (mp) REVERT: A 432 TRP cc_start: 0.7829 (m-90) cc_final: 0.6770 (m100) REVERT: A 710 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9116 (tt) REVERT: A 717 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7880 (mm-30) REVERT: A 719 GLN cc_start: 0.8356 (mt0) cc_final: 0.7966 (mt0) REVERT: A 750 TYR cc_start: 0.9107 (t80) cc_final: 0.8808 (t80) REVERT: A 1011 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9193 (tt) REVERT: A 1030 PHE cc_start: 0.8486 (t80) cc_final: 0.8155 (t80) outliers start: 30 outliers final: 21 residues processed: 139 average time/residue: 0.1758 time to fit residues: 36.0777 Evaluate side-chains 128 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1472 THR Chi-restraints excluded: chain A residue 1498 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 52 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8945 Z= 0.170 Angle : 0.536 8.771 12216 Z= 0.259 Chirality : 0.039 0.255 1497 Planarity : 0.004 0.053 1487 Dihedral : 8.425 161.976 1310 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.95 % Allowed : 14.88 % Favored : 82.17 % 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: 2.55 (0.25), residues: 1155 helix: 2.48 (0.19), residues: 787 sheet: 0.65 (0.68), residues: 60 loop : -0.18 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.005 0.001 HIS A1065 PHE 0.020 0.001 PHE A 991 TYR 0.007 0.001 TYR A 777 ARG 0.006 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.7811 (m-80) cc_final: 0.7251 (m-80) REVERT: A 297 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.6931 (mm) REVERT: A 425 LEU cc_start: 0.8862 (tp) cc_final: 0.8595 (mp) REVERT: A 432 TRP cc_start: 0.7715 (m-90) cc_final: 0.6780 (m100) REVERT: A 521 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8630 (ttmt) REVERT: A 710 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9097 (tt) REVERT: A 717 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 719 GLN cc_start: 0.8348 (mt0) cc_final: 0.7943 (mt0) REVERT: A 750 TYR cc_start: 0.9098 (t80) cc_final: 0.8844 (t80) REVERT: A 1011 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9189 (tt) REVERT: A 1030 PHE cc_start: 0.8368 (t80) cc_final: 0.8022 (t80) outliers start: 25 outliers final: 18 residues processed: 134 average time/residue: 0.1752 time to fit residues: 34.8418 Evaluate side-chains 128 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1472 THR Chi-restraints excluded: chain A residue 1498 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 0.0870 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8945 Z= 0.165 Angle : 0.541 7.842 12216 Z= 0.259 Chirality : 0.039 0.266 1497 Planarity : 0.004 0.052 1487 Dihedral : 8.255 160.236 1310 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.72 % Allowed : 15.94 % Favored : 81.35 % 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: 2.65 (0.25), residues: 1155 helix: 2.55 (0.19), residues: 787 sheet: 0.52 (0.66), residues: 65 loop : -0.09 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.005 0.001 HIS A1065 PHE 0.022 0.001 PHE A 991 TYR 0.006 0.001 TYR A 777 ARG 0.004 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.7756 (m-80) cc_final: 0.7196 (m-80) REVERT: A 297 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.6902 (mm) REVERT: A 402 MET cc_start: 0.7446 (ptm) cc_final: 0.7132 (ptm) REVERT: A 425 LEU cc_start: 0.8854 (tp) cc_final: 0.8598 (mp) REVERT: A 432 TRP cc_start: 0.7614 (m-90) cc_final: 0.6754 (m100) REVERT: A 521 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8604 (ttmt) REVERT: A 710 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9083 (tt) REVERT: A 717 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7871 (mm-30) REVERT: A 719 GLN cc_start: 0.8402 (mt0) cc_final: 0.8068 (mt0) REVERT: A 750 TYR cc_start: 0.9084 (t80) cc_final: 0.8809 (t80) REVERT: A 847 MET cc_start: 0.9125 (ttm) cc_final: 0.8920 (ttp) REVERT: A 1011 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9173 (tt) REVERT: A 1030 PHE cc_start: 0.8312 (t80) cc_final: 0.7942 (t80) REVERT: A 1071 LYS cc_start: 0.8593 (tppt) cc_final: 0.8367 (mmmm) REVERT: A 1259 ASN cc_start: 0.8674 (p0) cc_final: 0.8209 (t0) outliers start: 23 outliers final: 16 residues processed: 136 average time/residue: 0.1609 time to fit residues: 33.0137 Evaluate side-chains 133 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1472 THR Chi-restraints excluded: chain A residue 1498 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 0.0020 chunk 108 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 94 optimal weight: 0.1980 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8945 Z= 0.159 Angle : 0.539 7.713 12216 Z= 0.257 Chirality : 0.038 0.251 1497 Planarity : 0.004 0.052 1487 Dihedral : 8.114 158.616 1310 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.72 % Allowed : 16.41 % Favored : 80.87 % 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: 2.77 (0.25), residues: 1155 helix: 2.62 (0.19), residues: 781 sheet: 0.57 (0.65), residues: 65 loop : 0.05 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.004 0.001 HIS A1065 PHE 0.014 0.001 PHE A1395 TYR 0.006 0.001 TYR A 777 ARG 0.004 0.000 ARG A 804 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.7695 (m-80) cc_final: 0.7140 (m-80) REVERT: A 297 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.6851 (mm) REVERT: A 425 LEU cc_start: 0.8843 (tp) cc_final: 0.8600 (mp) REVERT: A 432 TRP cc_start: 0.7532 (m-90) cc_final: 0.6754 (m100) REVERT: A 710 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9062 (tt) REVERT: A 719 GLN cc_start: 0.8409 (mt0) cc_final: 0.8054 (mt0) REVERT: A 750 TYR cc_start: 0.9083 (t80) cc_final: 0.8809 (t80) REVERT: A 973 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7026 (ttm) REVERT: A 1011 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9224 (tt) REVERT: A 1030 PHE cc_start: 0.8215 (t80) cc_final: 0.7842 (t80) REVERT: A 1071 LYS cc_start: 0.8555 (tppt) cc_final: 0.8343 (mmmm) REVERT: A 1259 ASN cc_start: 0.8652 (p0) cc_final: 0.8210 (t0) outliers start: 23 outliers final: 17 residues processed: 135 average time/residue: 0.1619 time to fit residues: 33.0417 Evaluate side-chains 133 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1472 THR Chi-restraints excluded: chain A residue 1498 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 52 optimal weight: 0.0170 chunk 77 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 92 optimal weight: 0.0470 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.4916 ------------------------------------------------------------------------------- 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: 0.8212 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8945 Z= 0.158 Angle : 0.549 7.637 12216 Z= 0.259 Chirality : 0.039 0.287 1497 Planarity : 0.004 0.052 1487 Dihedral : 8.038 157.352 1309 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.24 % Allowed : 17.24 % Favored : 80.52 % 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: 2.69 (0.25), residues: 1155 helix: 2.56 (0.19), residues: 788 sheet: 0.61 (0.65), residues: 65 loop : -0.04 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.004 0.001 HIS A1065 PHE 0.024 0.001 PHE A 991 TYR 0.006 0.001 TYR A1250 ARG 0.004 0.000 ARG A 804 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.7665 (m-80) cc_final: 0.7127 (m-80) REVERT: A 297 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.6881 (mm) REVERT: A 425 LEU cc_start: 0.8850 (tp) cc_final: 0.8601 (mp) REVERT: A 432 TRP cc_start: 0.7455 (m-90) cc_final: 0.6697 (m100) REVERT: A 710 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9041 (tt) REVERT: A 719 GLN cc_start: 0.8426 (mt0) cc_final: 0.8078 (mt0) REVERT: A 750 TYR cc_start: 0.9066 (t80) cc_final: 0.8806 (t80) REVERT: A 862 VAL cc_start: 0.9288 (t) cc_final: 0.9019 (p) REVERT: A 871 TYR cc_start: 0.7617 (m-80) cc_final: 0.7260 (m-80) REVERT: A 1011 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9223 (tt) REVERT: A 1030 PHE cc_start: 0.8138 (t80) cc_final: 0.7751 (t80) REVERT: A 1071 LYS cc_start: 0.8504 (tppt) cc_final: 0.8264 (mmmm) REVERT: A 1259 ASN cc_start: 0.8648 (p0) cc_final: 0.8225 (t0) REVERT: A 1395 PHE cc_start: 0.7833 (m-80) cc_final: 0.7563 (m-80) outliers start: 19 outliers final: 16 residues processed: 139 average time/residue: 0.1719 time to fit residues: 35.6997 Evaluate side-chains 143 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1472 THR Chi-restraints excluded: chain A residue 1498 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.141807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107014 restraints weight = 14136.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110541 restraints weight = 6756.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112854 restraints weight = 4311.011| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8945 Z= 0.378 Angle : 0.670 7.739 12216 Z= 0.322 Chirality : 0.043 0.229 1497 Planarity : 0.004 0.052 1487 Dihedral : 8.219 154.207 1309 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.95 % Allowed : 17.36 % Favored : 79.69 % 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: 2.26 (0.25), residues: 1155 helix: 2.19 (0.18), residues: 789 sheet: 0.81 (0.66), residues: 60 loop : -0.17 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1214 HIS 0.006 0.001 HIS A1001 PHE 0.014 0.002 PHE A 569 TYR 0.016 0.002 TYR A 777 ARG 0.004 0.001 ARG A1150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1802.29 seconds wall clock time: 33 minutes 52.08 seconds (2032.08 seconds total)