Starting phenix.real_space_refine on Fri Dec 8 10:22:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg3_31964/12_2023/7vg3_31964.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg3_31964/12_2023/7vg3_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_31964/12_2023/7vg3_31964.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg3_31964/12_2023/7vg3_31964.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg3_31964/12_2023/7vg3_31964.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vg3_31964/12_2023/7vg3_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.01, per 1000 atoms: 0.62 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: 3.74 Conformation dependent library (CDL) restraints added in 1.5 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: 2.94 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: 3.07 Time building geometry restraints manager: 3.96 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: 4911 35.41 - 70.82: 145 70.82 - 106.23: 14 106.23 - 141.64: 0 141.64 - 177.06: 1 Dihedral angle restraints: 5071 sinusoidal: 2566 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 5068 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.120 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 29.550 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.650 ------------------------------------------------------------------------------- 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 : 15.378 177.055 3443 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 : 0.828 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 16 residues processed: 151 average time/residue: 0.2439 time to fit residues: 47.6621 Evaluate side-chains 88 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.835 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0994 time to fit residues: 3.7272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 0.0370 chunk 43 optimal weight: 0.0870 chunk 53 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.8240 ------------------------------------------------------------------------------- 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 A1197 HIS A1260 ASN A1460 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2033 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= 0.216 Angle : 0.680 8.921 11658 Z= 0.347 Chirality : 0.041 0.173 1365 Planarity : 0.006 0.085 1263 Dihedral : 14.633 176.470 1781 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.22 % Favored : 90.54 % Rotamer: Outliers : 4.21 % Allowed : 13.03 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.25), residues: 846 helix: -1.79 (0.25), residues: 332 sheet: -1.26 (0.50), residues: 115 loop : -3.03 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1078 HIS 0.012 0.001 HIS A 756 PHE 0.026 0.002 PHE A 759 TYR 0.018 0.001 TYR A1181 ARG 0.006 0.001 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 124 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 0.872 Fit side-chains outliers start: 32 outliers final: 12 residues processed: 122 average time/residue: 0.1628 time to fit residues: 29.3007 Evaluate side-chains 83 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0778 time to fit residues: 2.8236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 83 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 GLN A1029 HIS A1196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8407 Z= 0.229 Angle : 0.649 9.786 11658 Z= 0.332 Chirality : 0.041 0.160 1365 Planarity : 0.005 0.061 1263 Dihedral : 14.524 176.331 1781 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.17 % Favored : 89.72 % Rotamer: Outliers : 4.08 % Allowed : 15.53 % Favored : 80.39 % 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: -2.71 (0.27), residues: 846 helix: -0.85 (0.28), residues: 331 sheet: -1.47 (0.49), residues: 112 loop : -2.76 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1078 HIS 0.013 0.001 HIS A 756 PHE 0.018 0.002 PHE A 759 TYR 0.015 0.001 TYR A1181 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 108 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 77 time to evaluate : 0.860 Fit side-chains outliers start: 31 outliers final: 17 residues processed: 102 average time/residue: 0.1892 time to fit residues: 27.3762 Evaluate side-chains 87 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0798 time to fit residues: 3.6284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 938 HIS A1482 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2868 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= 0.302 Angle : 0.686 7.714 11658 Z= 0.349 Chirality : 0.042 0.164 1365 Planarity : 0.005 0.053 1263 Dihedral : 14.524 175.743 1781 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.28 % Favored : 89.60 % Rotamer: Outliers : 4.08 % Allowed : 16.97 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.28), residues: 846 helix: -0.50 (0.29), residues: 333 sheet: -1.66 (0.48), residues: 115 loop : -2.65 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1078 HIS 0.013 0.001 HIS A 756 PHE 0.020 0.002 PHE A 657 TYR 0.014 0.002 TYR A1358 ARG 0.009 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 107 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 76 time to evaluate : 0.960 Fit side-chains outliers start: 31 outliers final: 14 residues processed: 101 average time/residue: 0.2115 time to fit residues: 29.6239 Evaluate side-chains 85 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0837 time to fit residues: 3.2592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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** A 977 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3076 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= 0.152 Angle : 0.605 9.718 11658 Z= 0.307 Chirality : 0.038 0.163 1365 Planarity : 0.004 0.044 1263 Dihedral : 14.368 177.454 1781 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.46 % Favored : 90.43 % Rotamer: Outliers : 2.24 % Allowed : 18.82 % Favored : 78.95 % 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: -1.91 (0.29), residues: 846 helix: -0.00 (0.30), residues: 335 sheet: -1.25 (0.50), residues: 113 loop : -2.44 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1078 HIS 0.008 0.001 HIS A 756 PHE 0.014 0.001 PHE A 657 TYR 0.011 0.001 TYR A1181 ARG 0.013 0.001 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 98 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.853 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 91 average time/residue: 0.1813 time to fit residues: 24.0555 Evaluate side-chains 83 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0827 time to fit residues: 2.4713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 21 optimal weight: 0.0770 chunk 89 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 overall best weight: 2.9944 ------------------------------------------------------------------------------- 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** A 977 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3169 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= 0.295 Angle : 0.667 8.777 11658 Z= 0.341 Chirality : 0.041 0.183 1365 Planarity : 0.005 0.041 1263 Dihedral : 14.411 175.649 1781 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.23 % Favored : 88.65 % Rotamer: Outliers : 1.84 % Allowed : 21.05 % Favored : 77.11 % 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: -1.84 (0.29), residues: 846 helix: 0.18 (0.30), residues: 329 sheet: -1.59 (0.47), residues: 119 loop : -2.35 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1078 HIS 0.011 0.001 HIS A 756 PHE 0.013 0.002 PHE A 657 TYR 0.015 0.002 TYR A1358 ARG 0.010 0.001 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 85 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.861 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 81 average time/residue: 0.1847 time to fit residues: 21.6508 Evaluate side-chains 74 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0838 time to fit residues: 2.4452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** A 977 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3283 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= 0.196 Angle : 0.619 9.379 11658 Z= 0.314 Chirality : 0.039 0.161 1365 Planarity : 0.004 0.040 1263 Dihedral : 14.353 176.730 1781 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.69 % Favored : 90.19 % Rotamer: Outliers : 2.11 % Allowed : 20.79 % Favored : 77.11 % 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: -1.64 (0.29), residues: 846 helix: 0.34 (0.30), residues: 333 sheet: -1.32 (0.48), residues: 115 loop : -2.32 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1078 HIS 0.009 0.001 HIS A 756 PHE 0.012 0.001 PHE A 989 TYR 0.010 0.001 TYR A1181 ARG 0.010 0.000 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 90 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.773 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 85 average time/residue: 0.1865 time to fit residues: 22.8644 Evaluate side-chains 76 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.859 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0768 time to fit residues: 2.0058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.9337 > 50: distance: 27 - 33: 4.570 distance: 33 - 34: 9.185 distance: 34 - 35: 12.162 distance: 34 - 37: 4.047 distance: 35 - 36: 12.694 distance: 35 - 44: 5.868 distance: 37 - 38: 3.850 distance: 38 - 39: 6.979 distance: 38 - 40: 6.818 distance: 39 - 41: 6.642 distance: 40 - 42: 4.853 distance: 41 - 43: 5.836 distance: 42 - 43: 5.300 distance: 44 - 45: 4.120 distance: 45 - 46: 17.653 distance: 45 - 48: 26.732 distance: 46 - 47: 11.121 distance: 46 - 52: 10.750 distance: 48 - 49: 11.657 distance: 49 - 50: 5.955 distance: 49 - 51: 4.613 distance: 52 - 53: 8.564 distance: 53 - 54: 21.115 distance: 53 - 56: 35.343 distance: 54 - 55: 13.773 distance: 54 - 61: 31.014 distance: 56 - 57: 21.323 distance: 57 - 58: 9.672 distance: 58 - 59: 21.316 distance: 58 - 60: 17.970 distance: 61 - 62: 15.086 distance: 62 - 63: 30.983 distance: 62 - 65: 30.834 distance: 63 - 64: 21.284 distance: 63 - 70: 11.921 distance: 65 - 66: 20.388 distance: 66 - 67: 17.465 distance: 67 - 68: 10.372 distance: 67 - 69: 10.399 distance: 70 - 71: 8.708 distance: 71 - 72: 4.350 distance: 72 - 73: 13.938 distance: 74 - 75: 13.699 distance: 75 - 76: 7.098 distance: 76 - 77: 5.673 distance: 78 - 79: 8.712 distance: 79 - 80: 3.521 distance: 79 - 82: 6.619 distance: 80 - 81: 13.793 distance: 80 - 85: 17.601 distance: 82 - 83: 3.614 distance: 82 - 84: 3.237 distance: 85 - 86: 5.920 distance: 86 - 87: 11.499 distance: 86 - 89: 9.693 distance: 87 - 88: 12.942 distance: 87 - 96: 24.364 distance: 89 - 90: 4.393 distance: 90 - 91: 5.812 distance: 91 - 92: 4.656 distance: 96 - 97: 3.788 distance: 97 - 98: 12.821 distance: 98 - 99: 9.372 distance: 98 - 105: 10.702 distance: 100 - 101: 8.515 distance: 101 - 102: 10.295 distance: 103 - 104: 8.274 distance: 105 - 106: 30.777 distance: 106 - 107: 27.607 distance: 106 - 109: 24.776 distance: 107 - 108: 26.550 distance: 109 - 110: 14.104 distance: 110 - 111: 5.221 distance: 111 - 112: 10.544 distance: 116 - 117: 19.850 distance: 117 - 118: 15.482 distance: 117 - 120: 22.463 distance: 118 - 119: 20.802 distance: 118 - 125: 25.330 distance: 120 - 121: 8.836 distance: 121 - 122: 5.073 distance: 122 - 123: 35.083 distance: 123 - 124: 15.529