Starting phenix.real_space_refine on Tue Feb 13 23:40:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg3_31964/02_2024/7vg3_31964.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg3_31964/02_2024/7vg3_31964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg3_31964/02_2024/7vg3_31964.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg3_31964/02_2024/7vg3_31964.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg3_31964/02_2024/7vg3_31964.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg3_31964/02_2024/7vg3_31964.pdb" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 P 61 5.49 5 S 36 5.16 5 C 4913 2.51 5 N 1392 2.21 5 O 1713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 627": "NH1" <-> "NH2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "A ARG 933": "NH1" <-> "NH2" Residue "A ARG 948": "NH1" <-> "NH2" Residue "A ARG 968": "NH1" <-> "NH2" Residue "A ARG 1013": "NH1" <-> "NH2" Residue "A ARG 1057": "NH1" <-> "NH2" Residue "A ARG 1076": "NH1" <-> "NH2" Residue "A TYR 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1207": "OE1" <-> "OE2" Residue "A ARG 1215": "NH1" <-> "NH2" Residue "A ARG 1237": "NH1" <-> "NH2" Residue "A ARG 1255": "NH1" <-> "NH2" Residue "A ARG 1303": "NH1" <-> "NH2" Residue "A GLU 1402": "OE1" <-> "OE2" Residue "A ARG 1423": "NH1" <-> "NH2" Residue "A ARG 1478": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8118 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 6800 Classifications: {'peptide': 860} Link IDs: {'PTRANS': 37, 'TRANS': 822} Chain breaks: 6 Chain: "C" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 636 Classifications: {'RNA': 30} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 15, 'rna3p_pyr': 13} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "D" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 679 Classifications: {'RNA': 32} Modifications used: {'5*END': 1, 'rna3p_pur': 17, 'rna3p_pyr': 15} Link IDs: {'rna3p': 31} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3363 SG CYS A1091 37.744 55.435 37.136 1.00 56.47 S ATOM 3378 SG CYS A1093 41.924 55.592 37.534 1.00 61.85 S ATOM 3582 SG CYS A1119 39.383 53.825 40.277 1.00 46.05 S Time building chain proxies: 5.25, per 1000 atoms: 0.65 Number of scatterers: 8118 At special positions: 0 Unit cell: (115.92, 91.56, 99.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Ca 2 19.99 S 36 16.00 P 61 15.00 O 1713 8.00 N 1392 7.00 C 4913 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: 3.52 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" ND1 HIS A1123 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1093 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1119 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1091 " Number of angles added : 3 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1628 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 7 sheets defined 39.3% alpha, 12.7% beta 14 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 710 through 725 removed outlier: 3.730A pdb=" N TYR A 719 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 720 " --> pdb=" O LYS A 716 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 795 removed outlier: 3.609A pdb=" N ILE A 782 " --> pdb=" O ASP A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 888 removed outlier: 3.730A pdb=" N TYR A 888 " --> pdb=" O PHE A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 961 through 972 removed outlier: 4.449A pdb=" N HIS A 967 " --> pdb=" O PRO A 963 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG A 968 " --> pdb=" O SER A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 983 removed outlier: 3.547A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 998 removed outlier: 3.680A pdb=" N ILE A 996 " --> pdb=" O SER A 992 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 998 " --> pdb=" O THR A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1034 removed outlier: 3.520A pdb=" N GLU A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A1017 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A1020 " --> pdb=" O LEU A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1050 removed outlier: 3.689A pdb=" N GLN A1045 " --> pdb=" O GLN A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1060 removed outlier: 3.669A pdb=" N THR A1060 " --> pdb=" O HIS A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1063 No H-bonds generated for 'chain 'A' and resid 1061 through 1063' Processing helix chain 'A' and resid 1064 through 1068 removed outlier: 3.822A pdb=" N ILE A1068 " --> pdb=" O GLN A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1146 removed outlier: 3.516A pdb=" N ILE A1139 " --> pdb=" O ALA A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1159 removed outlier: 3.824A pdb=" N MET A1154 " --> pdb=" O ALA A1150 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A1155 " --> pdb=" O SER A1151 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A1159 " --> pdb=" O MET A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1176 Processing helix chain 'A' and resid 1190 through 1196 removed outlier: 4.243A pdb=" N LYS A1194 " --> pdb=" O GLU A1190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A1196 " --> pdb=" O GLU A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1208 removed outlier: 3.725A pdb=" N LEU A1205 " --> pdb=" O ALA A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1243 removed outlier: 3.786A pdb=" N SER A1229 " --> pdb=" O PHE A1225 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A1240 " --> pdb=" O THR A1236 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A1241 " --> pdb=" O ARG A1237 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A1242 " --> pdb=" O HIS A1238 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A1243 " --> pdb=" O LEU A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1259 removed outlier: 3.847A pdb=" N ASP A1253 " --> pdb=" O GLY A1249 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1271 removed outlier: 3.576A pdb=" N VAL A1269 " --> pdb=" O ALA A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1277 removed outlier: 3.597A pdb=" N HIS A1276 " --> pdb=" O LEU A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1293 removed outlier: 3.711A pdb=" N GLN A1287 " --> pdb=" O VAL A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1329 removed outlier: 3.729A pdb=" N ALA A1322 " --> pdb=" O VAL A1318 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A1323 " --> pdb=" O GLU A1319 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A1326 " --> pdb=" O ALA A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1344 Proline residue: A1342 - end of helix Processing helix chain 'A' and resid 1356 through 1369 removed outlier: 3.871A pdb=" N SER A1367 " --> pdb=" O GLU A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1422 removed outlier: 3.659A pdb=" N GLN A1419 " --> pdb=" O HIS A1415 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A1422 " --> pdb=" O THR A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1488 Processing helix chain 'A' and resid 1544 through 1562 removed outlier: 3.540A pdb=" N GLU A1561 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG A1562 " --> pdb=" O TYR A1558 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 629 through 631 removed outlier: 3.639A pdb=" N ARG A1124 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 687 through 691 removed outlier: 3.564A pdb=" N SER A 700 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 658 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 650 " --> pdb=" O LEU A 709 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 687 through 691 removed outlier: 3.564A pdb=" N SER A 700 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 658 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 670 " --> pdb=" O VAL A 766 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 938 through 941 removed outlier: 3.515A pdb=" N MET A 900 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 901 " --> pdb=" O GLU A 858 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE A 856 " --> pdb=" O LYS A 903 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 845 " --> pdb=" O TYR A 854 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 856 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU A 843 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL A 844 " --> pdb=" O ILE A 949 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1372 through 1377 removed outlier: 3.628A pdb=" N GLN A1384 " --> pdb=" O SER A1377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1372 through 1377 removed outlier: 3.628A pdb=" N GLN A1384 " --> pdb=" O SER A1377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1494 through 1498 removed outlier: 3.950A pdb=" N THR A1522 " --> pdb=" O SER A1498 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A1537 " --> pdb=" O ILE A1525 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A1535 " --> pdb=" O LEU A1527 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2151 1.34 - 1.46: 2021 1.46 - 1.58: 4059 1.58 - 1.70: 122 1.70 - 1.82: 54 Bond restraints: 8407 Sorted by residual: bond pdb=" P U C 1 " pdb=" OP3 U C 1 " ideal model delta sigma weight residual 1.480 1.606 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" N SER A1212 " pdb=" CA SER A1212 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.69e+00 bond pdb=" N ASN A1405 " pdb=" CA ASN A1405 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.48e+00 bond pdb=" N HIS A1197 " pdb=" CA HIS A1197 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.18e-02 7.18e+03 8.43e+00 bond pdb=" N LEU A 746 " pdb=" CA LEU A 746 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.43e+00 ... (remaining 8402 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.13: 494 106.13 - 113.17: 4591 113.17 - 120.22: 3186 120.22 - 127.26: 3180 127.26 - 134.31: 207 Bond angle restraints: 11658 Sorted by residual: angle pdb=" N ALA A 758 " pdb=" CA ALA A 758 " pdb=" C ALA A 758 " ideal model delta sigma weight residual 114.75 107.13 7.62 1.26e+00 6.30e-01 3.65e+01 angle pdb=" N PRO A 757 " pdb=" CA PRO A 757 " pdb=" C PRO A 757 " ideal model delta sigma weight residual 112.47 123.73 -11.26 2.06e+00 2.36e-01 2.99e+01 angle pdb=" C HIS A1211 " pdb=" N SER A1212 " pdb=" CA SER A1212 " ideal model delta sigma weight residual 121.54 131.66 -10.12 1.91e+00 2.74e-01 2.81e+01 angle pdb=" N ALA A1072 " pdb=" CA ALA A1072 " pdb=" C ALA A1072 " ideal model delta sigma weight residual 114.75 108.32 6.43 1.26e+00 6.30e-01 2.60e+01 angle pdb=" C THR A1404 " pdb=" N ASN A1405 " pdb=" CA ASN A1405 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 ... (remaining 11653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 4957 35.41 - 70.82: 171 70.82 - 106.23: 14 106.23 - 141.64: 0 141.64 - 177.06: 1 Dihedral angle restraints: 5143 sinusoidal: 2638 harmonic: 2505 Sorted by residual: dihedral pdb=" O4' U C 1 " pdb=" C1' U C 1 " pdb=" N1 U C 1 " pdb=" C2 U C 1 " ideal model delta sinusoidal sigma weight residual -128.00 49.06 -177.06 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA PRO A1356 " pdb=" C PRO A1356 " pdb=" N PRO A1357 " pdb=" CA PRO A1357 " ideal model delta harmonic sigma weight residual -180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA PHE A 830 " pdb=" C PHE A 830 " pdb=" N ALA A 831 " pdb=" CA ALA A 831 " ideal model delta harmonic sigma weight residual 180.00 153.96 26.04 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 5140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1115 0.069 - 0.138: 195 0.138 - 0.207: 44 0.207 - 0.276: 7 0.276 - 0.345: 4 Chirality restraints: 1365 Sorted by residual: chirality pdb=" CA PRO A 757 " pdb=" N PRO A 757 " pdb=" C PRO A 757 " pdb=" CB PRO A 757 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA PHE A 759 " pdb=" N PHE A 759 " pdb=" C PHE A 759 " pdb=" CB PHE A 759 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CB VAL A 951 " pdb=" CA VAL A 951 " pdb=" CG1 VAL A 951 " pdb=" CG2 VAL A 951 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 1362 not shown) Planarity restraints: 1263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 756 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.25e+00 pdb=" C HIS A 756 " 0.053 2.00e-02 2.50e+03 pdb=" O HIS A 756 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO A 757 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 851 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C GLY A 851 " -0.046 2.00e-02 2.50e+03 pdb=" O GLY A 851 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG A 852 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 951 " 0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 952 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 952 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 952 " 0.036 5.00e-02 4.00e+02 ... (remaining 1260 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 31 2.53 - 3.12: 5552 3.12 - 3.71: 12743 3.71 - 4.31: 16753 4.31 - 4.90: 26612 Nonbonded interactions: 61691 Sorted by model distance: nonbonded pdb=" OP1 U C 25 " pdb="CA CA A2002 " model vdw 1.935 2.510 nonbonded pdb=" OE2 GLU A1224 " pdb="CA CA A2002 " model vdw 2.153 2.510 nonbonded pdb=" OP1 A D 9 " pdb="CA CA A2001 " model vdw 2.221 2.510 nonbonded pdb=" OE2 GLU A1015 " pdb="CA CA A2001 " model vdw 2.248 2.510 nonbonded pdb=" OG SER A 855 " pdb=" O LYS A 903 " model vdw 2.271 2.440 ... (remaining 61686 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: 0.770 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: 2.190 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 30.390 Find NCS groups from input model: 0.210 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 : 0.006 0.126 8407 Z= 0.405 Angle : 1.148 11.258 11658 Z= 0.654 Chirality : 0.060 0.345 1365 Planarity : 0.007 0.064 1263 Dihedral : 16.120 177.055 3515 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.76 % Favored : 88.65 % Rotamer: Outliers : 5.13 % Allowed : 7.37 % Favored : 87.50 % Cbeta Deviations : 0.25 % 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: -4.51 (0.22), residues: 846 helix: -3.42 (0.19), residues: 331 sheet: -0.92 (0.57), residues: 87 loop : -3.12 (0.24), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A1078 HIS 0.010 0.002 HIS A 631 PHE 0.025 0.003 PHE A 989 TYR 0.019 0.002 TYR A1370 ARG 0.011 0.001 ARG A 968 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 126 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 624 SER cc_start: 0.8856 (p) cc_final: 0.8599 (t) REVERT: A 731 LYS cc_start: 0.8648 (ptmt) cc_final: 0.8279 (ptmm) REVERT: A 746 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8747 (tt) REVERT: A 914 ASP cc_start: 0.8155 (p0) cc_final: 0.7852 (p0) REVERT: A 966 MET cc_start: 0.8071 (mtm) cc_final: 0.7847 (mtp) REVERT: A 969 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8575 (tm) REVERT: A 1112 THR cc_start: 0.8111 (p) cc_final: 0.7861 (t) REVERT: A 1213 SER cc_start: 0.7024 (OUTLIER) cc_final: 0.6731 (p) REVERT: A 1403 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.6952 (pp30) REVERT: A 1492 MET cc_start: 0.8223 (tpp) cc_final: 0.7900 (tpt) REVERT: A 1526 THR cc_start: 0.9043 (t) cc_final: 0.8747 (p) outliers start: 39 outliers final: 16 residues processed: 151 average time/residue: 0.2494 time to fit residues: 48.7478 Evaluate side-chains 95 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 75 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1206 LYS Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain A residue 1219 SER Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1403 GLN Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1407 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.0870 chunk 53 optimal weight: 0.0270 chunk 83 optimal weight: 6.9990 overall best weight: 1.1618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 GLN A 783 ASN A 967 HIS A 977 GLN A 988 ASN ** A1029 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 ASN A1110 ASN A1260 ASN A1403 GLN ** A1405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1460 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8407 Z= 0.173 Angle : 0.649 8.877 11658 Z= 0.332 Chirality : 0.040 0.166 1365 Planarity : 0.005 0.084 1263 Dihedral : 16.829 177.584 1895 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.10 % Favored : 90.66 % Rotamer: Outliers : 5.26 % Allowed : 12.11 % Favored : 82.63 % 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: -3.50 (0.25), residues: 846 helix: -1.88 (0.25), residues: 343 sheet: -1.30 (0.50), residues: 109 loop : -3.05 (0.26), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1078 HIS 0.012 0.001 HIS A 756 PHE 0.014 0.001 PHE A 759 TYR 0.018 0.001 TYR A1181 ARG 0.008 0.000 ARG A1215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 98 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 624 SER cc_start: 0.8727 (p) cc_final: 0.8477 (t) REVERT: A 731 LYS cc_start: 0.8670 (ptmt) cc_final: 0.8294 (ptmm) REVERT: A 759 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.6807 (m-80) REVERT: A 914 ASP cc_start: 0.8247 (p0) cc_final: 0.7832 (p0) REVERT: A 966 MET cc_start: 0.7901 (mtm) cc_final: 0.7624 (mtp) REVERT: A 983 ASP cc_start: 0.7433 (t70) cc_final: 0.7220 (p0) outliers start: 40 outliers final: 21 residues processed: 133 average time/residue: 0.1720 time to fit residues: 33.2221 Evaluate side-chains 95 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 73 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 657 PHE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1403 GLN Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1529 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 GLN A 938 HIS A1196 GLN A1197 HIS ** A1405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1482 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8407 Z= 0.346 Angle : 0.718 10.212 11658 Z= 0.370 Chirality : 0.043 0.176 1365 Planarity : 0.005 0.066 1263 Dihedral : 16.448 175.665 1879 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.99 % Favored : 88.89 % Rotamer: Outliers : 6.05 % Allowed : 14.47 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.27), residues: 846 helix: -1.00 (0.28), residues: 332 sheet: -1.55 (0.49), residues: 115 loop : -2.78 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 643 HIS 0.015 0.002 HIS A 756 PHE 0.023 0.002 PHE A 759 TYR 0.021 0.002 TYR A1358 ARG 0.008 0.001 ARG A1215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 77 time to evaluate : 0.879 Fit side-chains REVERT: A 624 SER cc_start: 0.8857 (p) cc_final: 0.8569 (t) REVERT: A 731 LYS cc_start: 0.8754 (ptmt) cc_final: 0.8358 (ptmm) REVERT: A 760 MET cc_start: 0.7101 (mtp) cc_final: 0.6729 (mmm) REVERT: A 828 ILE cc_start: 0.1565 (OUTLIER) cc_final: 0.1175 (tp) REVERT: A 914 ASP cc_start: 0.8285 (p0) cc_final: 0.7781 (p0) REVERT: A 966 MET cc_start: 0.8025 (mtm) cc_final: 0.7578 (mtp) REVERT: A 1174 ASN cc_start: 0.6279 (m110) cc_final: 0.6062 (m110) REVERT: A 1175 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.5850 (mtp85) REVERT: A 1221 GLU cc_start: 0.7825 (pm20) cc_final: 0.7576 (pm20) outliers start: 46 outliers final: 32 residues processed: 116 average time/residue: 0.1894 time to fit residues: 30.7080 Evaluate side-chains 107 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 73 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 657 PHE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1379 ASP Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1529 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 0.0570 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 overall best weight: 3.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8407 Z= 0.296 Angle : 0.665 9.592 11658 Z= 0.341 Chirality : 0.042 0.201 1365 Planarity : 0.005 0.055 1263 Dihedral : 16.234 176.268 1868 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.69 % Favored : 90.19 % Rotamer: Outliers : 6.71 % Allowed : 15.00 % Favored : 78.29 % 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: -2.51 (0.28), residues: 846 helix: -0.55 (0.29), residues: 333 sheet: -1.65 (0.49), residues: 115 loop : -2.68 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1078 HIS 0.012 0.001 HIS A 756 PHE 0.015 0.002 PHE A 759 TYR 0.014 0.002 TYR A1181 ARG 0.010 0.001 ARG A1215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 71 time to evaluate : 0.863 Fit side-chains REVERT: A 828 ILE cc_start: 0.1680 (OUTLIER) cc_final: 0.1302 (tp) REVERT: A 914 ASP cc_start: 0.8247 (p0) cc_final: 0.7710 (p0) REVERT: A 966 MET cc_start: 0.7996 (mtm) cc_final: 0.7466 (mtp) REVERT: A 1174 ASN cc_start: 0.6337 (m110) cc_final: 0.6093 (m110) REVERT: A 1509 ILE cc_start: 0.6248 (OUTLIER) cc_final: 0.5820 (mp) REVERT: A 1542 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6010 (ptp-170) outliers start: 51 outliers final: 33 residues processed: 115 average time/residue: 0.2020 time to fit residues: 32.1437 Evaluate side-chains 104 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 68 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 657 PHE Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1379 ASP Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1542 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1029 HIS A1405 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8407 Z= 0.167 Angle : 0.601 9.443 11658 Z= 0.306 Chirality : 0.039 0.152 1365 Planarity : 0.004 0.046 1263 Dihedral : 16.094 177.635 1864 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.93 % Favored : 89.95 % Rotamer: Outliers : 6.05 % Allowed : 17.24 % Favored : 76.71 % 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: -2.09 (0.28), residues: 846 helix: -0.15 (0.29), residues: 339 sheet: -1.56 (0.49), residues: 111 loop : -2.49 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1078 HIS 0.009 0.001 HIS A 756 PHE 0.011 0.001 PHE A 989 TYR 0.012 0.001 TYR A1181 ARG 0.011 0.000 ARG A1532 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 77 time to evaluate : 0.908 Fit side-chains REVERT: A 624 SER cc_start: 0.8786 (p) cc_final: 0.8572 (t) REVERT: A 760 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.5955 (mmm) REVERT: A 762 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8175 (mm) REVERT: A 828 ILE cc_start: 0.1710 (OUTLIER) cc_final: 0.1390 (tp) REVERT: A 914 ASP cc_start: 0.8258 (p0) cc_final: 0.7868 (p0) REVERT: A 966 MET cc_start: 0.7909 (mtm) cc_final: 0.7288 (mtm) REVERT: A 1174 ASN cc_start: 0.6450 (m110) cc_final: 0.6208 (m110) REVERT: A 1175 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.5922 (mtp85) REVERT: A 1379 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.6875 (p0) REVERT: A 1509 ILE cc_start: 0.6192 (OUTLIER) cc_final: 0.5756 (mp) REVERT: A 1542 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6264 (ptp-170) outliers start: 46 outliers final: 31 residues processed: 112 average time/residue: 0.1887 time to fit residues: 29.6571 Evaluate side-chains 110 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 72 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 657 PHE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1379 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1542 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.0010 chunk 21 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 0.0970 chunk 46 optimal weight: 0.0980 chunk 85 optimal weight: 10.0000 overall best weight: 0.8388 ------------------------------------------------------------------------------- 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: 0.8277 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8407 Z= 0.148 Angle : 0.588 11.638 11658 Z= 0.295 Chirality : 0.038 0.161 1365 Planarity : 0.004 0.042 1263 Dihedral : 16.006 177.707 1863 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.98 % Favored : 90.90 % Rotamer: Outliers : 6.05 % Allowed : 17.89 % Favored : 76.05 % 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: -1.81 (0.29), residues: 846 helix: 0.17 (0.30), residues: 337 sheet: -1.39 (0.49), residues: 112 loop : -2.41 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1078 HIS 0.008 0.001 HIS A 756 PHE 0.011 0.001 PHE A 989 TYR 0.011 0.001 TYR A1181 ARG 0.011 0.000 ARG A1215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 78 time to evaluate : 0.868 Fit side-chains REVERT: A 624 SER cc_start: 0.8857 (p) cc_final: 0.8556 (t) REVERT: A 630 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8454 (mt) REVERT: A 914 ASP cc_start: 0.8270 (p0) cc_final: 0.7881 (p0) REVERT: A 966 MET cc_start: 0.7954 (mtm) cc_final: 0.7329 (mtm) REVERT: A 1174 ASN cc_start: 0.6386 (m110) cc_final: 0.6155 (m110) REVERT: A 1175 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.5960 (mtp85) REVERT: A 1191 LEU cc_start: 0.8794 (tt) cc_final: 0.8476 (tt) REVERT: A 1379 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.6895 (p0) REVERT: A 1509 ILE cc_start: 0.6191 (OUTLIER) cc_final: 0.5977 (mp) REVERT: A 1542 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.6110 (ptp-170) outliers start: 46 outliers final: 28 residues processed: 113 average time/residue: 0.1930 time to fit residues: 30.5445 Evaluate side-chains 108 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 75 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1379 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1542 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 chunk 65 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8407 Z= 0.304 Angle : 0.667 10.329 11658 Z= 0.337 Chirality : 0.041 0.157 1365 Planarity : 0.005 0.044 1263 Dihedral : 16.030 176.108 1863 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.11 % Favored : 88.77 % Rotamer: Outliers : 6.45 % Allowed : 18.29 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.29), residues: 846 helix: 0.26 (0.30), residues: 332 sheet: -1.57 (0.46), residues: 119 loop : -2.41 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1078 HIS 0.011 0.001 HIS A 756 PHE 0.014 0.002 PHE A 652 TYR 0.014 0.002 TYR A1358 ARG 0.011 0.001 ARG A1215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 69 time to evaluate : 0.844 Fit side-chains REVERT: A 630 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8521 (mt) REVERT: A 762 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8309 (mm) REVERT: A 914 ASP cc_start: 0.8252 (p0) cc_final: 0.7788 (p0) REVERT: A 966 MET cc_start: 0.8030 (mtm) cc_final: 0.7488 (mtm) REVERT: A 1175 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6130 (mtp85) REVERT: A 1379 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.6921 (p0) REVERT: A 1509 ILE cc_start: 0.6142 (OUTLIER) cc_final: 0.5712 (mp) REVERT: A 1542 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6000 (ptp-170) outliers start: 49 outliers final: 34 residues processed: 107 average time/residue: 0.1960 time to fit residues: 29.9451 Evaluate side-chains 106 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 66 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1379 ASP Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1542 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 0.0060 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 84 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8407 Z= 0.199 Angle : 0.632 10.278 11658 Z= 0.316 Chirality : 0.039 0.163 1365 Planarity : 0.004 0.039 1263 Dihedral : 15.988 177.029 1863 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 6.05 % Allowed : 18.16 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.29), residues: 846 helix: 0.30 (0.30), residues: 339 sheet: -1.47 (0.47), residues: 117 loop : -2.32 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1078 HIS 0.009 0.001 HIS A 756 PHE 0.011 0.001 PHE A 989 TYR 0.010 0.001 TYR A1181 ARG 0.009 0.001 ARG A1193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 73 time to evaluate : 0.891 Fit side-chains REVERT: A 630 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8445 (mt) REVERT: A 760 MET cc_start: 0.6599 (mtp) cc_final: 0.6367 (mtp) REVERT: A 914 ASP cc_start: 0.8232 (p0) cc_final: 0.7760 (p0) REVERT: A 966 MET cc_start: 0.7946 (mtm) cc_final: 0.7270 (mtm) REVERT: A 1175 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6159 (mtp85) REVERT: A 1379 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.6924 (p0) REVERT: A 1509 ILE cc_start: 0.6157 (OUTLIER) cc_final: 0.5716 (mp) REVERT: A 1542 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.6454 (ptp-170) outliers start: 46 outliers final: 33 residues processed: 106 average time/residue: 0.2055 time to fit residues: 30.1565 Evaluate side-chains 108 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 70 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 662 ASN Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1379 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1542 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 25 optimal weight: 0.0980 chunk 74 optimal weight: 7.9990 chunk 78 optimal weight: 0.0010 chunk 82 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1460 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8407 Z= 0.178 Angle : 0.625 11.821 11658 Z= 0.310 Chirality : 0.039 0.168 1365 Planarity : 0.004 0.037 1263 Dihedral : 15.938 177.388 1863 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 5.39 % Allowed : 19.08 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.29), residues: 846 helix: 0.40 (0.30), residues: 337 sheet: -1.33 (0.48), residues: 116 loop : -2.32 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1078 HIS 0.008 0.001 HIS A 756 PHE 0.012 0.001 PHE A 989 TYR 0.012 0.001 TYR A1034 ARG 0.008 0.000 ARG A1215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 74 time to evaluate : 0.911 Fit side-chains REVERT: A 630 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8430 (mt) REVERT: A 760 MET cc_start: 0.6634 (mtp) cc_final: 0.6418 (mtp) REVERT: A 762 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8151 (mm) REVERT: A 914 ASP cc_start: 0.8243 (p0) cc_final: 0.7779 (p0) REVERT: A 966 MET cc_start: 0.7932 (mtm) cc_final: 0.7265 (mtm) REVERT: A 1175 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6161 (mtp85) REVERT: A 1379 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.6940 (p0) REVERT: A 1509 ILE cc_start: 0.6161 (OUTLIER) cc_final: 0.5746 (mp) REVERT: A 1542 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.6269 (ptp-170) outliers start: 41 outliers final: 31 residues processed: 100 average time/residue: 0.2010 time to fit residues: 28.1341 Evaluate side-chains 109 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 72 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 662 ASN Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1379 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1542 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 0.0060 chunk 44 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 overall best weight: 2.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1460 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8407 Z= 0.253 Angle : 0.664 11.609 11658 Z= 0.329 Chirality : 0.040 0.182 1365 Planarity : 0.004 0.039 1263 Dihedral : 15.908 176.391 1861 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 4.74 % Allowed : 20.00 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.29), residues: 846 helix: 0.40 (0.30), residues: 339 sheet: -1.50 (0.47), residues: 116 loop : -2.27 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1078 HIS 0.010 0.001 HIS A 756 PHE 0.019 0.002 PHE A 759 TYR 0.014 0.001 TYR A1291 ARG 0.008 0.000 ARG A1215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 69 time to evaluate : 0.794 Fit side-chains REVERT: A 630 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8505 (mt) REVERT: A 762 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8230 (mm) REVERT: A 914 ASP cc_start: 0.8227 (p0) cc_final: 0.7758 (p0) REVERT: A 966 MET cc_start: 0.7974 (mtm) cc_final: 0.7303 (mtm) REVERT: A 1175 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6164 (mtp85) REVERT: A 1379 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.6920 (p0) REVERT: A 1509 ILE cc_start: 0.6060 (OUTLIER) cc_final: 0.5611 (mp) REVERT: A 1542 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6371 (ptp-170) outliers start: 36 outliers final: 28 residues processed: 95 average time/residue: 0.2176 time to fit residues: 28.8445 Evaluate side-chains 102 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 68 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1379 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1542 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.0170 chunk 75 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.132700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107900 restraints weight = 14257.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.110948 restraints weight = 8350.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112956 restraints weight = 5994.831| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8407 Z= 0.198 Angle : 0.641 11.637 11658 Z= 0.316 Chirality : 0.039 0.177 1365 Planarity : 0.004 0.039 1263 Dihedral : 15.843 177.034 1859 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 5.13 % Allowed : 20.00 % Favored : 74.87 % 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: -1.51 (0.29), residues: 846 helix: 0.50 (0.30), residues: 339 sheet: -1.53 (0.47), residues: 116 loop : -2.23 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1078 HIS 0.009 0.001 HIS A 756 PHE 0.014 0.001 PHE A 759 TYR 0.008 0.001 TYR A1181 ARG 0.008 0.000 ARG A1215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1618.82 seconds wall clock time: 30 minutes 11.64 seconds (1811.64 seconds total)