Starting phenix.real_space_refine on Thu Mar 14 18:45:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1j_33563/03_2024/7y1j_33563_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1j_33563/03_2024/7y1j_33563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1j_33563/03_2024/7y1j_33563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1j_33563/03_2024/7y1j_33563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1j_33563/03_2024/7y1j_33563_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1j_33563/03_2024/7y1j_33563_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.138 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 6 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 6129 2.51 5 N 1573 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1445": "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: 9487 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1209, 9487 Unusual residues: {' MG': 2, 'ATP': 2, 'BJX': 1} Classifications: {'peptide': 1204, 'undetermined': 5} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 35, 'TRANS': 1168, None: 5} Not linked: pdbres="MET A1542 " pdbres="ATP A1601 " Not linked: pdbres="ATP A1601 " pdbres="ATP A1602 " Not linked: pdbres="ATP A1602 " pdbres=" MG A1603 " Not linked: pdbres=" MG A1603 " pdbres=" MG A1604 " Not linked: pdbres=" MG A1604 " pdbres="BJX A1605 " Chain breaks: 6 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 61 Time building chain proxies: 5.72, per 1000 atoms: 0.60 Number of scatterers: 9487 At special positions: 0 Unit cell: (70.5324, 102.939, 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 51 16.00 P 6 15.00 Mg 2 11.99 O 1726 8.00 N 1573 7.00 C 6129 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: 3.22 Conformation dependent library (CDL) restraints added in 1.5 seconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 6 sheets defined 66.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 240 removed outlier: 4.647A pdb=" N THR A 233 " --> pdb=" O TRP A 230 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 237 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 239 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 257 through 273 Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 295 through 311 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 348 through 394 Processing helix chain 'A' and resid 404 through 415 removed outlier: 4.627A pdb=" N GLY A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 496 Proline residue: A 429 - end of helix removed outlier: 3.993A pdb=" N TRP A 432 " --> pdb=" O CYS A 428 " (cutoff:3.500A) Proline residue: A 435 - end of helix removed outlier: 7.932A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N SER A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.691A 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 557 removed outlier: 3.653A pdb=" N THR A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) Proline residue: A 544 - end of helix Processing helix chain 'A' and resid 565 through 606 removed outlier: 4.243A pdb=" N THR A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) Proline residue: A 581 - end of helix removed outlier: 4.677A pdb=" N SER A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 762 through 767 Processing helix chain 'A' and resid 774 through 783 Processing helix chain 'A' and resid 787 through 791 Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 810 through 823 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 854 through 857 No H-bonds generated for 'chain 'A' and resid 854 through 857' Processing helix chain 'A' and resid 869 through 874 removed outlier: 3.927A 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 922 removed outlier: 4.070A pdb=" N LYS A 919 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 937 removed outlier: 3.649A pdb=" N MET A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 970 No H-bonds generated for 'chain 'A' and resid 967 through 970' Processing helix chain 'A' and resid 975 through 985 removed outlier: 4.197A pdb=" N GLY A 985 " --> pdb=" O TYR A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1017 removed outlier: 3.616A pdb=" N GLU A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1073 removed outlier: 3.604A pdb=" N GLU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A1070 " --> pdb=" O HIS A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1082 Processing helix chain 'A' and resid 1085 through 1101 removed outlier: 4.025A pdb=" N ASP A1095 " --> pdb=" O ARG A1091 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1127 Processing helix chain 'A' and resid 1129 through 1175 removed outlier: 3.577A pdb=" N ALA A1136 " --> pdb=" O ILE A1133 " (cutoff:3.500A) Proline residue: A1137 - end of helix removed outlier: 4.265A pdb=" N TYR A1148 " --> pdb=" O ILE A1145 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE A1149 " --> pdb=" O GLN A1146 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER A1153 " --> pdb=" O ARG A1150 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN A1157 " --> pdb=" O LYS A1154 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU A1165 " --> pdb=" O SER A1162 " (cutoff:3.500A) Proline residue: A1166 - end of helix Processing helix chain 'A' and resid 1178 through 1184 Processing helix chain 'A' and resid 1187 through 1236 Processing helix chain 'A' and resid 1241 through 1283 removed outlier: 3.885A pdb=" N THR A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A1257 " --> pdb=" O THR A1253 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TRP A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1355 Processing helix chain 'A' and resid 1378 through 1384 removed outlier: 3.511A pdb=" N ARG A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1403 Processing helix chain 'A' and resid 1411 through 1420 Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1433 through 1435 No H-bonds generated for 'chain 'A' and resid 1433 through 1435' Processing helix chain 'A' and resid 1447 through 1461 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 1541 Processing sheet with id= A, first strand: chain 'A' and resid 724 through 727 removed outlier: 6.968A pdb=" N ILE A 691 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS A 669 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 689 " --> pdb=" O LYS A 669 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 886 through 890 removed outlier: 7.200A pdb=" N ALA A 880 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU A 889 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 878 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 862 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE A 699 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 864 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY A 701 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1330 through 1332 Processing sheet with id= D, first strand: chain 'A' and resid 1519 through 1524 removed outlier: 6.764A pdb=" N VAL A1514 " --> pdb=" O VAL A1521 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS A1523 " --> pdb=" O VAL A1512 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL A1512 " --> pdb=" O CYS A1523 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A1386 " --> pdb=" O ILE A1467 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASP A1469 " --> pdb=" O SER A1386 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE A1388 " --> pdb=" O ASP A1469 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 674 through 676 removed outlier: 6.825A pdb=" N SER A 676 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N THR A 720 " --> pdb=" O SER A 676 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1325 through 1328 removed outlier: 5.326A pdb=" N LEU A1313 " --> pdb=" O HIS A1327 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A1363 " --> pdb=" O CYS A1314 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARG A1316 " --> pdb=" O ILE A1361 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE A1361 " --> pdb=" O ARG A1316 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 3.56 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: 1499 1.31 - 1.43: 2484 1.43 - 1.56: 5599 1.56 - 1.68: 10 1.68 - 1.81: 83 Bond restraints: 9675 Sorted by residual: bond pdb=" C16 BJX A1605 " pdb=" N1 BJX A1605 " ideal model delta sigma weight residual 1.344 1.446 -0.102 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C21 BJX A1605 " pdb=" O1 BJX A1605 " ideal model delta sigma weight residual 1.347 1.397 -0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" O BJX A1605 " pdb=" C16 BJX A1605 " ideal model delta sigma weight residual 1.221 1.181 0.040 2.00e-02 2.50e+03 3.99e+00 bond pdb=" N BJX A1605 " pdb=" C6 BJX A1605 " ideal model delta sigma weight residual 1.412 1.450 -0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" C17 BJX A1605 " pdb=" C18 BJX A1605 " ideal model delta sigma weight residual 1.498 1.523 -0.025 2.00e-02 2.50e+03 1.62e+00 ... (remaining 9670 not shown) Histogram of bond angle deviations from ideal: 98.92 - 107.10: 249 107.10 - 115.28: 6041 115.28 - 123.45: 6611 123.45 - 131.63: 218 131.63 - 139.81: 27 Bond angle restraints: 13146 Sorted by residual: angle pdb=" N GLY A1177 " pdb=" CA GLY A1177 " pdb=" C GLY A1177 " ideal model delta sigma weight residual 115.63 110.45 5.18 1.49e+00 4.50e-01 1.21e+01 angle pdb=" CA GLY A1177 " pdb=" C GLY A1177 " pdb=" N LEU A1178 " ideal model delta sigma weight residual 118.64 115.13 3.51 1.24e+00 6.50e-01 8.01e+00 angle pdb=" CA GLY A1177 " pdb=" C GLY A1177 " pdb=" O GLY A1177 " ideal model delta sigma weight residual 118.95 121.53 -2.58 1.00e+00 1.00e+00 6.65e+00 angle pdb=" O2 BJX A1605 " pdb=" C24 BJX A1605 " pdb=" O3 BJX A1605 " ideal model delta sigma weight residual 126.98 120.05 6.93 3.00e+00 1.11e-01 5.34e+00 angle pdb=" C1 BJX A1605 " pdb=" N BJX A1605 " pdb=" C6 BJX A1605 " ideal model delta sigma weight residual 117.04 110.14 6.90 3.00e+00 1.11e-01 5.29e+00 ... (remaining 13141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.97: 5681 31.97 - 63.95: 103 63.95 - 95.92: 8 95.92 - 127.89: 0 127.89 - 159.86: 1 Dihedral angle restraints: 5793 sinusoidal: 2289 harmonic: 3504 Sorted by residual: dihedral pdb=" O BJX A1605 " pdb=" C16 BJX A1605 " pdb=" C17 BJX A1605 " pdb=" C18 BJX A1605 " ideal model delta sinusoidal sigma weight residual 10.31 -149.55 159.86 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" CA LEU A 448 " pdb=" C LEU A 448 " pdb=" N LEU A 449 " pdb=" CA LEU A 449 " ideal model delta harmonic sigma weight residual -180.00 -164.06 -15.94 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" N GLN A 870 " pdb=" CA GLN A 870 " pdb=" CB GLN A 870 " pdb=" CG GLN A 870 " ideal model delta sinusoidal sigma weight residual 60.00 0.10 59.90 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1133 0.037 - 0.074: 312 0.074 - 0.111: 94 0.111 - 0.148: 19 0.148 - 0.185: 2 Chirality restraints: 1560 Sorted by residual: chirality pdb=" C5 BJX A1605 " pdb=" C7 BJX A1605 " pdb=" C8 BJX A1605 " pdb=" N1 BJX A1605 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA CYS A 428 " pdb=" N CYS A 428 " pdb=" C CYS A 428 " pdb=" CB CYS A 428 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA ILE A1361 " pdb=" N ILE A1361 " pdb=" C ILE A1361 " pdb=" CB ILE A1361 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1557 not shown) Planarity restraints: 1613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1103 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A1104 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A1104 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1104 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A1526 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A1527 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A1527 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1527 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1143 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C TYR A1143 " -0.023 2.00e-02 2.50e+03 pdb=" O TYR A1143 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE A1144 " 0.008 2.00e-02 2.50e+03 ... (remaining 1610 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 62 2.56 - 3.14: 7787 3.14 - 3.73: 15428 3.73 - 4.31: 21661 4.31 - 4.90: 36664 Nonbonded interactions: 81602 Sorted by model distance: nonbonded pdb=" OG SER A1349 " pdb="MG MG A1603 " model vdw 1.971 2.170 nonbonded pdb=" OG SER A 708 " pdb="MG MG A1604 " model vdw 1.972 2.170 nonbonded pdb=" OE1 GLN A 753 " pdb="MG MG A1604 " model vdw 1.978 2.170 nonbonded pdb=" O1G ATP A1601 " pdb="MG MG A1604 " model vdw 2.166 2.170 nonbonded pdb=" O2B ATP A1601 " pdb="MG MG A1604 " model vdw 2.168 2.170 ... (remaining 81597 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: 0.910 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: 5.100 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.180 Find NCS groups from input model: 0.260 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 0.102 9675 Z= 0.242 Angle : 0.509 6.932 13146 Z= 0.273 Chirality : 0.039 0.185 1560 Planarity : 0.004 0.034 1613 Dihedral : 12.137 159.862 3523 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.69 % Allowed : 3.35 % Favored : 95.96 % 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: 2.20 (0.24), residues: 1190 helix: 2.04 (0.18), residues: 808 sheet: 0.57 (0.65), residues: 65 loop : 0.23 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1214 HIS 0.005 0.001 HIS A1001 PHE 0.013 0.001 PHE A 569 TYR 0.013 0.001 TYR A 228 ARG 0.003 0.000 ARG A1457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.7879 (mttm) cc_final: 0.7640 (mmtt) REVERT: A 235 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7990 (mp) REVERT: A 375 GLU cc_start: 0.7437 (tt0) cc_final: 0.7150 (tt0) REVERT: A 472 THR cc_start: 0.8678 (m) cc_final: 0.8477 (p) REVERT: A 514 SER cc_start: 0.8568 (t) cc_final: 0.8222 (p) REVERT: A 525 SER cc_start: 0.8045 (t) cc_final: 0.7718 (m) REVERT: A 527 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7371 (tttt) REVERT: A 607 LEU cc_start: 0.8151 (mp) cc_final: 0.7497 (pp) REVERT: A 782 ASP cc_start: 0.7396 (m-30) cc_final: 0.7158 (m-30) REVERT: A 797 ASP cc_start: 0.8117 (m-30) cc_final: 0.7755 (m-30) REVERT: A 853 LYS cc_start: 0.8435 (tttt) cc_final: 0.7970 (tttm) REVERT: A 976 LYS cc_start: 0.8079 (mttt) cc_final: 0.7622 (mmpt) REVERT: A 1004 ILE cc_start: 0.8367 (mt) cc_final: 0.8162 (mm) REVERT: A 1055 TRP cc_start: 0.7288 (t60) cc_final: 0.6644 (t-100) REVERT: A 1100 ASP cc_start: 0.7924 (m-30) cc_final: 0.7665 (m-30) REVERT: A 1185 ARG cc_start: 0.7894 (mtp85) cc_final: 0.7587 (mtt-85) REVERT: A 1282 LEU cc_start: 0.7993 (mt) cc_final: 0.7774 (mt) REVERT: A 1307 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7039 (mt-10) REVERT: A 1312 ASP cc_start: 0.7486 (t70) cc_final: 0.6581 (t70) REVERT: A 1360 ASP cc_start: 0.7650 (t0) cc_final: 0.7113 (m-30) REVERT: A 1422 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8125 (mm-40) REVERT: A 1468 MET cc_start: 0.8954 (mtm) cc_final: 0.8720 (mtp) outliers start: 7 outliers final: 4 residues processed: 199 average time/residue: 1.1085 time to fit residues: 237.3524 Evaluate side-chains 148 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 1281 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN A 271 GLN A 478 GLN A 540 ASN ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1066 HIS A1288 ASN A1319 ASN A1425 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9675 Z= 0.204 Angle : 0.468 6.787 13146 Z= 0.240 Chirality : 0.038 0.165 1560 Planarity : 0.004 0.038 1613 Dihedral : 10.551 164.151 1382 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.65 % Allowed : 8.47 % Favored : 87.88 % 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: 2.18 (0.24), residues: 1190 helix: 2.02 (0.18), residues: 821 sheet: 0.69 (0.69), residues: 60 loop : 0.11 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1214 HIS 0.004 0.001 HIS A1001 PHE 0.012 0.001 PHE A 569 TYR 0.012 0.001 TYR A 532 ARG 0.007 0.000 ARG A1413 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 0.977 Fit side-chains REVERT: A 225 LYS cc_start: 0.8027 (mttm) cc_final: 0.7665 (mmtt) REVERT: A 235 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7979 (mp) REVERT: A 241 LYS cc_start: 0.8048 (pttm) cc_final: 0.7432 (tttm) REVERT: A 375 GLU cc_start: 0.7401 (tt0) cc_final: 0.7158 (tt0) REVERT: A 425 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8166 (tp) REVERT: A 485 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8389 (p) REVERT: A 514 SER cc_start: 0.8582 (t) cc_final: 0.8246 (p) REVERT: A 520 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6749 (mpm) REVERT: A 525 SER cc_start: 0.8016 (t) cc_final: 0.7689 (m) REVERT: A 527 LYS cc_start: 0.7919 (ttpt) cc_final: 0.7397 (tttt) REVERT: A 672 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7595 (t160) REVERT: A 782 ASP cc_start: 0.7418 (m-30) cc_final: 0.7174 (m-30) REVERT: A 797 ASP cc_start: 0.8061 (m-30) cc_final: 0.7763 (m-30) REVERT: A 833 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: A 853 LYS cc_start: 0.8548 (tttt) cc_final: 0.8106 (ttpt) REVERT: A 973 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7581 (tpt) REVERT: A 976 LYS cc_start: 0.8076 (mttt) cc_final: 0.7631 (mmpt) REVERT: A 1055 TRP cc_start: 0.7265 (t60) cc_final: 0.6612 (t-100) REVERT: A 1100 ASP cc_start: 0.7872 (m-30) cc_final: 0.7626 (m-30) REVERT: A 1185 ARG cc_start: 0.7967 (mtp85) cc_final: 0.7616 (mtt-85) REVERT: A 1307 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7014 (mt-10) REVERT: A 1360 ASP cc_start: 0.7440 (t0) cc_final: 0.7055 (m-30) REVERT: A 1422 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8146 (mm-40) REVERT: A 1494 ARG cc_start: 0.7780 (mtt-85) cc_final: 0.7575 (mtt90) outliers start: 37 outliers final: 10 residues processed: 165 average time/residue: 1.1028 time to fit residues: 196.0852 Evaluate side-chains 154 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1281 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9675 Z= 0.198 Angle : 0.455 6.557 13146 Z= 0.234 Chirality : 0.038 0.165 1560 Planarity : 0.003 0.034 1613 Dihedral : 10.178 163.947 1382 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.25 % Allowed : 10.94 % Favored : 85.81 % 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: 2.25 (0.24), residues: 1190 helix: 2.09 (0.18), residues: 820 sheet: 0.68 (0.70), residues: 60 loop : 0.12 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1214 HIS 0.004 0.001 HIS A1001 PHE 0.019 0.001 PHE A 552 TYR 0.017 0.001 TYR A 532 ARG 0.006 0.000 ARG A1413 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 1.125 Fit side-chains REVERT: A 225 LYS cc_start: 0.8023 (mttm) cc_final: 0.7692 (mmtt) REVERT: A 241 LYS cc_start: 0.7980 (pttm) cc_final: 0.7415 (tttm) REVERT: A 485 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8393 (p) REVERT: A 514 SER cc_start: 0.8588 (t) cc_final: 0.8253 (p) REVERT: A 520 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6755 (mpm) REVERT: A 525 SER cc_start: 0.8037 (t) cc_final: 0.7671 (m) REVERT: A 527 LYS cc_start: 0.7912 (ttpt) cc_final: 0.7374 (tttt) REVERT: A 672 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7547 (t160) REVERT: A 774 ARG cc_start: 0.7573 (tpt170) cc_final: 0.7321 (tpt170) REVERT: A 778 LYS cc_start: 0.7918 (tptt) cc_final: 0.7657 (tmtm) REVERT: A 782 ASP cc_start: 0.7384 (m-30) cc_final: 0.7071 (m-30) REVERT: A 797 ASP cc_start: 0.8059 (m-30) cc_final: 0.7759 (m-30) REVERT: A 833 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7579 (m-30) REVERT: A 853 LYS cc_start: 0.8581 (tttt) cc_final: 0.8132 (ttpt) REVERT: A 973 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7518 (tpt) REVERT: A 976 LYS cc_start: 0.8109 (mttt) cc_final: 0.7661 (mmpt) REVERT: A 1055 TRP cc_start: 0.7262 (t60) cc_final: 0.6579 (t-100) REVERT: A 1100 ASP cc_start: 0.7864 (m-30) cc_final: 0.7624 (m-30) REVERT: A 1185 ARG cc_start: 0.7958 (mtp85) cc_final: 0.7613 (mtt-85) REVERT: A 1307 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7033 (mt-10) REVERT: A 1319 ASN cc_start: 0.7307 (m-40) cc_final: 0.7066 (m110) REVERT: A 1360 ASP cc_start: 0.7609 (t0) cc_final: 0.7136 (m-30) REVERT: A 1422 GLN cc_start: 0.8339 (mm-40) cc_final: 0.8117 (mm-40) outliers start: 33 outliers final: 8 residues processed: 158 average time/residue: 1.1416 time to fit residues: 194.1667 Evaluate side-chains 148 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1281 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A 686 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1279 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9675 Z= 0.277 Angle : 0.495 6.528 13146 Z= 0.254 Chirality : 0.040 0.168 1560 Planarity : 0.004 0.039 1613 Dihedral : 10.079 165.673 1379 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.55 % Allowed : 11.53 % Favored : 84.93 % 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: 2.04 (0.24), residues: 1190 helix: 1.93 (0.18), residues: 819 sheet: 0.60 (0.69), residues: 60 loop : 0.07 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1214 HIS 0.006 0.001 HIS A1001 PHE 0.018 0.002 PHE A 569 TYR 0.021 0.001 TYR A 532 ARG 0.007 0.000 ARG A1494 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.086 Fit side-chains REVERT: A 225 LYS cc_start: 0.8052 (mttm) cc_final: 0.7713 (mmtt) REVERT: A 241 LYS cc_start: 0.8005 (pttm) cc_final: 0.7472 (tttm) REVERT: A 514 SER cc_start: 0.8604 (t) cc_final: 0.8198 (p) REVERT: A 525 SER cc_start: 0.8062 (t) cc_final: 0.7722 (m) REVERT: A 527 LYS cc_start: 0.7908 (ttpt) cc_final: 0.7395 (tttt) REVERT: A 672 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7583 (t160) REVERT: A 782 ASP cc_start: 0.7389 (m-30) cc_final: 0.7111 (m-30) REVERT: A 833 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: A 853 LYS cc_start: 0.8602 (tttt) cc_final: 0.8257 (ttpt) REVERT: A 893 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8232 (pttm) REVERT: A 973 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7568 (tpt) REVERT: A 976 LYS cc_start: 0.8160 (mttt) cc_final: 0.7729 (mmpt) REVERT: A 1055 TRP cc_start: 0.7254 (t60) cc_final: 0.6569 (t-100) REVERT: A 1100 ASP cc_start: 0.7906 (m-30) cc_final: 0.7637 (m-30) REVERT: A 1185 ARG cc_start: 0.7958 (mtp85) cc_final: 0.7601 (mtt-85) REVERT: A 1307 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7134 (mt-10) REVERT: A 1319 ASN cc_start: 0.7190 (m-40) cc_final: 0.6970 (m110) REVERT: A 1360 ASP cc_start: 0.7803 (t0) cc_final: 0.7346 (m-30) REVERT: A 1420 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7807 (mp) REVERT: A 1422 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8115 (mm-40) outliers start: 36 outliers final: 15 residues processed: 157 average time/residue: 1.1878 time to fit residues: 201.1627 Evaluate side-chains 154 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 893 LYS Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1420 ILE Chi-restraints excluded: chain A residue 1444 ASN Chi-restraints excluded: chain A residue 1525 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9675 Z= 0.206 Angle : 0.466 6.527 13146 Z= 0.241 Chirality : 0.038 0.165 1560 Planarity : 0.004 0.042 1613 Dihedral : 9.809 164.954 1379 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.15 % Allowed : 12.61 % Favored : 84.24 % 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: 2.21 (0.24), residues: 1190 helix: 2.07 (0.18), residues: 818 sheet: 0.65 (0.69), residues: 60 loop : 0.09 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1214 HIS 0.004 0.000 HIS A1001 PHE 0.017 0.001 PHE A1445 TYR 0.018 0.001 TYR A 532 ARG 0.009 0.000 ARG A1494 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 0.963 Fit side-chains REVERT: A 225 LYS cc_start: 0.8023 (mttm) cc_final: 0.7698 (mmtt) REVERT: A 241 LYS cc_start: 0.7849 (pttm) cc_final: 0.7434 (tttm) REVERT: A 485 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8398 (p) REVERT: A 514 SER cc_start: 0.8594 (t) cc_final: 0.8263 (p) REVERT: A 525 SER cc_start: 0.8049 (t) cc_final: 0.7682 (m) REVERT: A 527 LYS cc_start: 0.7893 (ttpt) cc_final: 0.7367 (tttt) REVERT: A 672 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7599 (t160) REVERT: A 782 ASP cc_start: 0.7368 (m-30) cc_final: 0.7079 (m-30) REVERT: A 833 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7595 (m-30) REVERT: A 853 LYS cc_start: 0.8614 (tttt) cc_final: 0.8251 (ttpt) REVERT: A 973 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7539 (tpt) REVERT: A 976 LYS cc_start: 0.8160 (mttt) cc_final: 0.7726 (mmpt) REVERT: A 1055 TRP cc_start: 0.7224 (t60) cc_final: 0.6572 (t-100) REVERT: A 1100 ASP cc_start: 0.7894 (m-30) cc_final: 0.7646 (m-30) REVERT: A 1185 ARG cc_start: 0.7941 (mtp85) cc_final: 0.7590 (mtt-85) REVERT: A 1307 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7087 (mt-10) REVERT: A 1360 ASP cc_start: 0.7754 (t0) cc_final: 0.7346 (m-30) REVERT: A 1422 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8108 (mm-40) outliers start: 32 outliers final: 15 residues processed: 158 average time/residue: 1.0926 time to fit residues: 186.1877 Evaluate side-chains 154 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1444 ASN Chi-restraints excluded: chain A residue 1525 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 0.0070 chunk 53 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9675 Z= 0.162 Angle : 0.445 6.549 13146 Z= 0.231 Chirality : 0.038 0.162 1560 Planarity : 0.003 0.044 1613 Dihedral : 9.530 164.137 1379 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.05 % Allowed : 13.10 % Favored : 83.84 % 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: 2.37 (0.24), residues: 1190 helix: 2.20 (0.18), residues: 817 sheet: 0.71 (0.69), residues: 60 loop : 0.12 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1214 HIS 0.003 0.000 HIS A1001 PHE 0.019 0.001 PHE A1445 TYR 0.016 0.001 TYR A 532 ARG 0.010 0.000 ARG A1494 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.021 Fit side-chains REVERT: A 225 LYS cc_start: 0.7984 (mttm) cc_final: 0.7685 (mmtt) REVERT: A 241 LYS cc_start: 0.7869 (pttm) cc_final: 0.7466 (tttm) REVERT: A 485 SER cc_start: 0.8615 (OUTLIER) cc_final: 0.8410 (p) REVERT: A 514 SER cc_start: 0.8578 (t) cc_final: 0.8319 (p) REVERT: A 520 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6769 (mpm) REVERT: A 525 SER cc_start: 0.8028 (t) cc_final: 0.7673 (m) REVERT: A 527 LYS cc_start: 0.7909 (ttpt) cc_final: 0.7390 (tttt) REVERT: A 672 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7521 (t160) REVERT: A 778 LYS cc_start: 0.7926 (tptt) cc_final: 0.7648 (tmtm) REVERT: A 782 ASP cc_start: 0.7359 (m-30) cc_final: 0.7072 (m-30) REVERT: A 797 ASP cc_start: 0.8055 (m-30) cc_final: 0.7744 (m-30) REVERT: A 853 LYS cc_start: 0.8657 (tttt) cc_final: 0.8328 (ttpt) REVERT: A 973 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7436 (tpt) REVERT: A 976 LYS cc_start: 0.8152 (mttt) cc_final: 0.7715 (mmpt) REVERT: A 1055 TRP cc_start: 0.7200 (t60) cc_final: 0.6559 (t-100) REVERT: A 1100 ASP cc_start: 0.7863 (m-30) cc_final: 0.7637 (m-30) REVERT: A 1185 ARG cc_start: 0.7917 (mtp85) cc_final: 0.7577 (mtt-85) REVERT: A 1307 GLU cc_start: 0.7276 (mt-10) cc_final: 0.7013 (mt-10) REVERT: A 1360 ASP cc_start: 0.7763 (t0) cc_final: 0.7345 (m-30) REVERT: A 1422 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8131 (mm-40) outliers start: 31 outliers final: 14 residues processed: 161 average time/residue: 1.0738 time to fit residues: 186.1774 Evaluate side-chains 156 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1444 ASN Chi-restraints excluded: chain A residue 1460 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A 686 ASN A 719 GLN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9675 Z= 0.219 Angle : 0.471 6.548 13146 Z= 0.243 Chirality : 0.039 0.165 1560 Planarity : 0.004 0.039 1613 Dihedral : 9.646 165.210 1379 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.15 % Allowed : 13.50 % Favored : 83.35 % 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: 2.26 (0.24), residues: 1190 helix: 2.11 (0.18), residues: 815 sheet: 0.72 (0.69), residues: 60 loop : 0.10 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1214 HIS 0.005 0.000 HIS A1001 PHE 0.018 0.001 PHE A1445 TYR 0.021 0.001 TYR A 532 ARG 0.009 0.000 ARG A1494 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.078 Fit side-chains REVERT: A 225 LYS cc_start: 0.8006 (mttm) cc_final: 0.7699 (mmtt) REVERT: A 241 LYS cc_start: 0.7843 (pttm) cc_final: 0.7428 (tttp) REVERT: A 485 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8402 (p) REVERT: A 487 GLU cc_start: 0.7141 (tt0) cc_final: 0.6939 (tt0) REVERT: A 514 SER cc_start: 0.8597 (t) cc_final: 0.8277 (p) REVERT: A 525 SER cc_start: 0.8028 (t) cc_final: 0.7651 (m) REVERT: A 527 LYS cc_start: 0.7932 (ttpt) cc_final: 0.7407 (tttt) REVERT: A 672 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7558 (t160) REVERT: A 778 LYS cc_start: 0.7934 (tptt) cc_final: 0.7628 (tmtm) REVERT: A 782 ASP cc_start: 0.7365 (m-30) cc_final: 0.7054 (m-30) REVERT: A 797 ASP cc_start: 0.8061 (m-30) cc_final: 0.7737 (m-30) REVERT: A 833 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: A 853 LYS cc_start: 0.8636 (tttt) cc_final: 0.8314 (ttpt) REVERT: A 973 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7548 (tpt) REVERT: A 976 LYS cc_start: 0.8161 (mttt) cc_final: 0.7711 (mmpt) REVERT: A 1055 TRP cc_start: 0.7222 (t60) cc_final: 0.6578 (t-100) REVERT: A 1100 ASP cc_start: 0.7859 (m-30) cc_final: 0.7620 (m-30) REVERT: A 1185 ARG cc_start: 0.7934 (mtp85) cc_final: 0.7586 (mtt-85) REVERT: A 1307 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7055 (mt-10) REVERT: A 1360 ASP cc_start: 0.7757 (t0) cc_final: 0.7346 (m-30) REVERT: A 1422 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8123 (mm-40) REVERT: A 1480 GLU cc_start: 0.6803 (tt0) cc_final: 0.6191 (mt-10) outliers start: 32 outliers final: 17 residues processed: 162 average time/residue: 1.0838 time to fit residues: 189.4851 Evaluate side-chains 163 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 142 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1444 ASN Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1525 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 0.0170 chunk 90 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9675 Z= 0.182 Angle : 0.454 6.543 13146 Z= 0.235 Chirality : 0.038 0.163 1560 Planarity : 0.003 0.042 1613 Dihedral : 9.573 164.899 1379 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.05 % Allowed : 13.69 % Favored : 83.25 % 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: 2.32 (0.24), residues: 1190 helix: 2.17 (0.18), residues: 814 sheet: 0.77 (0.69), residues: 60 loop : 0.07 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1214 HIS 0.004 0.000 HIS A1001 PHE 0.018 0.001 PHE A1445 TYR 0.019 0.001 TYR A 532 ARG 0.010 0.000 ARG A1494 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.088 Fit side-chains REVERT: A 225 LYS cc_start: 0.7991 (mttm) cc_final: 0.7692 (mmtt) REVERT: A 241 LYS cc_start: 0.7824 (pttm) cc_final: 0.7422 (tttm) REVERT: A 485 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8411 (p) REVERT: A 514 SER cc_start: 0.8578 (t) cc_final: 0.8268 (p) REVERT: A 525 SER cc_start: 0.8052 (t) cc_final: 0.7689 (m) REVERT: A 527 LYS cc_start: 0.7906 (ttpt) cc_final: 0.7378 (tttt) REVERT: A 672 ASN cc_start: 0.8175 (OUTLIER) cc_final: 0.7536 (t160) REVERT: A 778 LYS cc_start: 0.7935 (tptt) cc_final: 0.7639 (tmtm) REVERT: A 782 ASP cc_start: 0.7360 (m-30) cc_final: 0.7057 (m-30) REVERT: A 833 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: A 853 LYS cc_start: 0.8660 (tttt) cc_final: 0.8264 (ttpt) REVERT: A 973 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7449 (tpt) REVERT: A 976 LYS cc_start: 0.8161 (mttt) cc_final: 0.7698 (mmpt) REVERT: A 1055 TRP cc_start: 0.7211 (t60) cc_final: 0.6565 (t-100) REVERT: A 1100 ASP cc_start: 0.7854 (m-30) cc_final: 0.7625 (m-30) REVERT: A 1185 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7581 (mtt-85) REVERT: A 1307 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6989 (mt-10) REVERT: A 1360 ASP cc_start: 0.7730 (t0) cc_final: 0.7310 (m-30) REVERT: A 1422 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8099 (mm-40) REVERT: A 1480 GLU cc_start: 0.6802 (tt0) cc_final: 0.6181 (mt-10) outliers start: 31 outliers final: 16 residues processed: 160 average time/residue: 1.1046 time to fit residues: 190.3472 Evaluate side-chains 161 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1444 ASN Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1525 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A 686 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9675 Z= 0.195 Angle : 0.464 6.546 13146 Z= 0.239 Chirality : 0.038 0.164 1560 Planarity : 0.004 0.043 1613 Dihedral : 9.583 165.230 1379 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.66 % Allowed : 14.29 % Favored : 83.05 % 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: 2.27 (0.24), residues: 1190 helix: 2.15 (0.18), residues: 808 sheet: 0.77 (0.69), residues: 60 loop : 0.03 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1214 HIS 0.004 0.000 HIS A1001 PHE 0.019 0.001 PHE A1445 TYR 0.023 0.001 TYR A 532 ARG 0.010 0.000 ARG A1494 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 1.116 Fit side-chains REVERT: A 225 LYS cc_start: 0.7958 (mttm) cc_final: 0.7638 (mmtt) REVERT: A 241 LYS cc_start: 0.7884 (pttm) cc_final: 0.7464 (tttm) REVERT: A 514 SER cc_start: 0.8589 (t) cc_final: 0.8262 (p) REVERT: A 525 SER cc_start: 0.8070 (t) cc_final: 0.7705 (m) REVERT: A 527 LYS cc_start: 0.7919 (ttpt) cc_final: 0.7396 (tttt) REVERT: A 672 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7546 (t160) REVERT: A 778 LYS cc_start: 0.7942 (tptt) cc_final: 0.7642 (tmtm) REVERT: A 782 ASP cc_start: 0.7336 (m-30) cc_final: 0.7031 (m-30) REVERT: A 833 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7553 (m-30) REVERT: A 853 LYS cc_start: 0.8660 (tttt) cc_final: 0.8260 (ttpt) REVERT: A 973 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7497 (tpt) REVERT: A 976 LYS cc_start: 0.8161 (mttt) cc_final: 0.7694 (mmpt) REVERT: A 1055 TRP cc_start: 0.7215 (t60) cc_final: 0.6555 (t-100) REVERT: A 1100 ASP cc_start: 0.7860 (m-30) cc_final: 0.7617 (m-30) REVERT: A 1185 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7584 (mtt-85) REVERT: A 1307 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6996 (mt-10) REVERT: A 1360 ASP cc_start: 0.7658 (t0) cc_final: 0.7204 (m-30) REVERT: A 1393 ILE cc_start: 0.8691 (mt) cc_final: 0.8406 (tt) REVERT: A 1422 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8097 (mm-40) REVERT: A 1480 GLU cc_start: 0.6853 (tt0) cc_final: 0.6173 (mt-10) outliers start: 27 outliers final: 15 residues processed: 158 average time/residue: 1.1675 time to fit residues: 199.0321 Evaluate side-chains 157 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1444 ASN Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1525 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 119 optimal weight: 0.0060 chunk 110 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9675 Z= 0.172 Angle : 0.454 6.562 13146 Z= 0.234 Chirality : 0.038 0.162 1560 Planarity : 0.003 0.042 1613 Dihedral : 9.486 164.976 1379 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.07 % Allowed : 15.07 % Favored : 82.86 % 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: 2.32 (0.24), residues: 1190 helix: 2.21 (0.18), residues: 807 sheet: 0.79 (0.69), residues: 60 loop : 0.03 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 980 HIS 0.004 0.000 HIS A1001 PHE 0.019 0.001 PHE A1445 TYR 0.023 0.001 TYR A 532 ARG 0.010 0.000 ARG A1494 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 1.171 Fit side-chains REVERT: A 225 LYS cc_start: 0.7969 (mttm) cc_final: 0.7683 (mmtt) REVERT: A 241 LYS cc_start: 0.7835 (pttm) cc_final: 0.7405 (tttm) REVERT: A 514 SER cc_start: 0.8567 (t) cc_final: 0.8306 (p) REVERT: A 525 SER cc_start: 0.8148 (t) cc_final: 0.7760 (m) REVERT: A 527 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7360 (tttt) REVERT: A 672 ASN cc_start: 0.8121 (OUTLIER) cc_final: 0.7520 (t160) REVERT: A 778 LYS cc_start: 0.7945 (tptt) cc_final: 0.7658 (tmtm) REVERT: A 782 ASP cc_start: 0.7335 (m-30) cc_final: 0.7041 (m-30) REVERT: A 797 ASP cc_start: 0.8052 (m-30) cc_final: 0.7737 (m-30) REVERT: A 853 LYS cc_start: 0.8656 (tttt) cc_final: 0.8254 (ttpt) REVERT: A 973 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7430 (tpt) REVERT: A 976 LYS cc_start: 0.8124 (mttt) cc_final: 0.7677 (mmpt) REVERT: A 1055 TRP cc_start: 0.7190 (t60) cc_final: 0.6551 (t-100) REVERT: A 1100 ASP cc_start: 0.7989 (m-30) cc_final: 0.7737 (m-30) REVERT: A 1185 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7571 (mtt-85) REVERT: A 1307 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6928 (mt-10) REVERT: A 1360 ASP cc_start: 0.7650 (t0) cc_final: 0.7202 (m-30) REVERT: A 1393 ILE cc_start: 0.8722 (mt) cc_final: 0.8420 (tt) REVERT: A 1420 ILE cc_start: 0.8030 (mp) cc_final: 0.7749 (mt) REVERT: A 1422 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8088 (mm-40) REVERT: A 1425 ASN cc_start: 0.8055 (m110) cc_final: 0.7471 (p0) REVERT: A 1480 GLU cc_start: 0.6823 (tt0) cc_final: 0.6190 (mt-10) REVERT: A 1494 ARG cc_start: 0.7685 (mtt-85) cc_final: 0.7435 (mtt90) outliers start: 21 outliers final: 13 residues processed: 154 average time/residue: 1.1302 time to fit residues: 187.1480 Evaluate side-chains 152 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1444 ASN Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1525 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 0.0770 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A 686 ASN ** A 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.139725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.106372 restraints weight = 10326.292| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.60 r_work: 0.3011 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9675 Z= 0.226 Angle : 0.480 6.569 13146 Z= 0.247 Chirality : 0.039 0.165 1560 Planarity : 0.004 0.043 1613 Dihedral : 9.485 165.947 1376 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.87 % Allowed : 15.47 % Favored : 82.66 % 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: 2.18 (0.24), residues: 1190 helix: 2.08 (0.18), residues: 807 sheet: 0.74 (0.69), residues: 60 loop : 0.01 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1214 HIS 0.005 0.000 HIS A1001 PHE 0.019 0.001 PHE A1445 TYR 0.029 0.001 TYR A 532 ARG 0.010 0.000 ARG A1494 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3603.34 seconds wall clock time: 64 minutes 11.33 seconds (3851.33 seconds total)