Starting phenix.real_space_refine on Fri Feb 14 22:42:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ky9_23072/02_2025/7ky9_23072.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ky9_23072/02_2025/7ky9_23072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ky9_23072/02_2025/7ky9_23072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ky9_23072/02_2025/7ky9_23072.map" model { file = "/net/cci-nas-00/data/ceres_data/7ky9_23072/02_2025/7ky9_23072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ky9_23072/02_2025/7ky9_23072.cif" } resolution = 4.05 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= 0.002 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 2 5.21 5 S 53 5.16 5 C 6646 2.51 5 N 1690 2.21 5 O 1956 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10354 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 7229 Classifications: {'peptide': 910} Link IDs: {'PTRANS': 25, 'TRANS': 884} Chain breaks: 2 Chain: "B" Number of atoms: 2959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2959 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.32, per 1000 atoms: 0.61 Number of scatterers: 10354 At special positions: 0 Unit cell: (129.682, 114.814, 130.508, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 53 16.00 P 2 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 1956 8.00 N 1690 7.00 C 6646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Links applied ALPHA1-4 " NAG C 2 " - " MAN C 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B1001 " - " ASN B 298 " " NAG C 1 " - " ASN B 240 " " NAG D 1 " - " ASN B 256 " " NAG E 1 " - " ASN B 332 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 51.5% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 282 through 301 removed outlier: 3.600A pdb=" N SER A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 619 removed outlier: 3.682A pdb=" N ARG A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 617 " --> pdb=" O GLY A 613 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 654 Processing helix chain 'A' and resid 661 through 679 removed outlier: 5.005A pdb=" N GLU A 667 " --> pdb=" O TYR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 700 through 705 removed outlier: 3.694A pdb=" N GLY A 704 " --> pdb=" O ASP A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 754 through 779 removed outlier: 3.511A pdb=" N SER A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 799 removed outlier: 3.873A pdb=" N VAL A 797 " --> pdb=" O SER A 793 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 798 " --> pdb=" O LYS A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 821 Processing helix chain 'A' and resid 843 through 857 Processing helix chain 'A' and resid 918 through 925 removed outlier: 4.200A pdb=" N ARG A 925 " --> pdb=" O VAL A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 949 Processing helix chain 'A' and resid 962 through 977 Processing helix chain 'A' and resid 983 through 995 Processing helix chain 'A' and resid 1013 through 1024 removed outlier: 3.796A pdb=" N SER A1017 " --> pdb=" O GLY A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1046 Processing helix chain 'A' and resid 1063 through 1069 removed outlier: 4.038A pdb=" N GLU A1067 " --> pdb=" O GLU A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1087 removed outlier: 3.930A pdb=" N VAL A1075 " --> pdb=" O ASP A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1104 Processing helix chain 'A' and resid 1116 through 1124 removed outlier: 3.782A pdb=" N LEU A1124 " --> pdb=" O LEU A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1137 Processing helix chain 'A' and resid 1149 through 1163 Processing helix chain 'A' and resid 1177 through 1183 Processing helix chain 'A' and resid 1193 through 1200 removed outlier: 3.792A pdb=" N GLN A1197 " --> pdb=" O GLU A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1210 No H-bonds generated for 'chain 'A' and resid 1208 through 1210' Processing helix chain 'A' and resid 1211 through 1218 removed outlier: 3.505A pdb=" N LEU A1217 " --> pdb=" O THR A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1249 Proline residue: A1232 - end of helix removed outlier: 3.712A pdb=" N VAL A1239 " --> pdb=" O PHE A1235 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE A1240 " --> pdb=" O TYR A1236 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHE A1241 " --> pdb=" O LYS A1237 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR A1242 " --> pdb=" O ASN A1238 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A1245 " --> pdb=" O PHE A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1255 removed outlier: 4.622A pdb=" N ASN A1253 " --> pdb=" O ILE A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1271 removed outlier: 3.775A pdb=" N PHE A1267 " --> pdb=" O THR A1263 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A1268 " --> pdb=" O TYR A1264 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ASN A1269 " --> pdb=" O LEU A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1274 through 1283 removed outlier: 3.931A pdb=" N ILE A1278 " --> pdb=" O SER A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1295 Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1309 through 1334 removed outlier: 3.502A pdb=" N PHE A1313 " --> pdb=" O ASN A1309 " (cutoff:3.500A) Proline residue: A1331 - end of helix Processing helix chain 'A' and resid 1350 through 1374 Processing helix chain 'A' and resid 1380 through 1399 removed outlier: 3.622A pdb=" N PHE A1384 " --> pdb=" O PHE A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1406 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1418 through 1447 removed outlier: 4.107A pdb=" N TRP A1422 " --> pdb=" O GLN A1418 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A1427 " --> pdb=" O ALA A1423 " (cutoff:3.500A) Proline residue: A1435 - end of helix Processing helix chain 'A' and resid 1449 through 1461 removed outlier: 3.733A pdb=" N GLY A1461 " --> pdb=" O MET A1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 71 through 98 Proline residue: B 77 - end of helix Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 267 through 273 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.879A pdb=" N GLU B 290 " --> pdb=" O PRO B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 removed outlier: 4.055A pdb=" N TRP B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.683A pdb=" N PHE B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 399 Processing helix chain 'B' and resid 405 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 1055 through 1057 removed outlier: 6.473A pdb=" N VAL A1113 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A1143 " --> pdb=" O LEU A1028 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A1030 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS A1145 " --> pdb=" O VAL A1030 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE A 709 " --> pdb=" O TRP A1029 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU A1031 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER A 711 " --> pdb=" O LEU A1031 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR A 708 " --> pdb=" O LEU A1169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 732 through 734 removed outlier: 5.520A pdb=" N VAL A 721 " --> pdb=" O ARG A1009 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A1009 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS A 725 " --> pdb=" O ALA A1005 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ALA A1005 " --> pdb=" O LYS A 725 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N CYS A 727 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY A1003 " --> pdb=" O CYS A 727 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 729 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N LEU A1001 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 956 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY A1003 " --> pdb=" O LEU A 954 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 954 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA A1005 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG A 952 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 858 through 860 Processing sheet with id=AA4, first strand: chain 'A' and resid 1188 through 1190 Processing sheet with id=AA5, first strand: chain 'A' and resid 1377 through 1378 Processing sheet with id=AA6, first strand: chain 'B' and resid 126 through 129 removed outlier: 6.897A pdb=" N VAL B 173 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE B 329 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 175 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 119 through 120 removed outlier: 4.035A pdb=" N GLN B 341 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR B 248 " --> pdb=" O GLN B 341 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP B 343 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLN B 246 " --> pdb=" O ASP B 343 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3265 1.34 - 1.46: 2385 1.46 - 1.58: 4853 1.58 - 1.69: 3 1.69 - 1.81: 80 Bond restraints: 10586 Sorted by residual: bond pdb=" F1 ALF A1702 " pdb="AL ALF A1702 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" F2 ALF A1702 " pdb="AL ALF A1702 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" F4 ALF A1702 " pdb="AL ALF A1702 " ideal model delta sigma weight residual 1.686 1.785 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" F3 ALF A1702 " pdb="AL ALF A1702 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C5 MAN C 3 " pdb=" O5 MAN C 3 " ideal model delta sigma weight residual 1.418 1.461 -0.043 2.00e-02 2.50e+03 4.61e+00 ... (remaining 10581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.24: 14356 14.24 - 28.48: 5 28.48 - 42.71: 0 42.71 - 56.95: 0 56.95 - 71.19: 2 Bond angle restraints: 14363 Sorted by residual: angle pdb=" F1 ALF A1702 " pdb="AL ALF A1702 " pdb=" F2 ALF A1702 " ideal model delta sigma weight residual 108.68 179.87 -71.19 3.00e+00 1.11e-01 5.63e+02 angle pdb=" F3 ALF A1702 " pdb="AL ALF A1702 " pdb=" F4 ALF A1702 " ideal model delta sigma weight residual 109.63 179.94 -70.31 3.00e+00 1.11e-01 5.49e+02 angle pdb=" F2 ALF A1702 " pdb="AL ALF A1702 " pdb=" F4 ALF A1702 " ideal model delta sigma weight residual 110.21 90.13 20.08 3.00e+00 1.11e-01 4.48e+01 angle pdb=" F2 ALF A1702 " pdb="AL ALF A1702 " pdb=" F3 ALF A1702 " ideal model delta sigma weight residual 109.59 89.89 19.70 3.00e+00 1.11e-01 4.31e+01 angle pdb=" F1 ALF A1702 " pdb="AL ALF A1702 " pdb=" F3 ALF A1702 " ideal model delta sigma weight residual 109.69 90.00 19.69 3.00e+00 1.11e-01 4.31e+01 ... (remaining 14358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.79: 6163 28.79 - 57.58: 208 57.58 - 86.38: 18 86.38 - 115.17: 5 115.17 - 143.96: 2 Dihedral angle restraints: 6396 sinusoidal: 2679 harmonic: 3717 Sorted by residual: dihedral pdb=" CB CYS B 110 " pdb=" SG CYS B 110 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual -86.00 -157.60 71.60 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" O1B ADP A1701 " pdb=" O3A ADP A1701 " pdb=" PB ADP A1701 " pdb=" PA ADP A1701 " ideal model delta sinusoidal sigma weight residual -60.00 83.96 -143.96 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O2A ADP A1701 " pdb=" O3A ADP A1701 " pdb=" PA ADP A1701 " pdb=" PB ADP A1701 " ideal model delta sinusoidal sigma weight residual -60.00 -150.44 90.44 1 2.00e+01 2.50e-03 2.42e+01 ... (remaining 6393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 1622 0.165 - 0.329: 2 0.329 - 0.494: 0 0.494 - 0.659: 0 0.659 - 0.824: 1 Chirality restraints: 1625 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 240 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" C1 MAN C 3 " pdb=" O4 NAG C 2 " pdb=" C2 MAN C 3 " pdb=" O5 MAN C 3 " both_signs ideal model delta sigma weight residual False 2.40 2.36 0.04 2.00e-02 2.50e+03 4.03e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.09e+00 ... (remaining 1622 not shown) Planarity restraints: 1806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 648 " 0.023 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP A 648 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP A 648 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 648 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 648 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 648 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 648 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 648 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 648 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 648 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 240 " -0.002 2.00e-02 2.50e+03 2.93e-02 1.07e+01 pdb=" CG ASN B 240 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 240 " -0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN B 240 " 0.037 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 240 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" C ASN B 240 " -0.042 2.00e-02 2.50e+03 pdb=" O ASN B 240 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP B 241 " 0.014 2.00e-02 2.50e+03 ... (remaining 1803 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1142 2.74 - 3.28: 11225 3.28 - 3.82: 17779 3.82 - 4.36: 20162 4.36 - 4.90: 33082 Nonbonded interactions: 83390 Sorted by model distance: nonbonded pdb=" OD1 ASP B 304 " pdb=" N ILE B 305 " model vdw 2.206 3.120 nonbonded pdb=" OE1 GLU A1193 " pdb=" F3 ALF A1702 " model vdw 2.216 2.990 nonbonded pdb=" OG1 THR A 718 " pdb=" O ARG A1009 " model vdw 2.218 3.040 nonbonded pdb=" O ARG B 188 " pdb=" OG SER B 192 " model vdw 2.224 3.040 nonbonded pdb=" CG2 THR A1342 " pdb=" O LEU A1346 " model vdw 2.244 3.460 ... (remaining 83385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 26.650 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 10586 Z= 0.244 Angle : 1.140 71.188 14363 Z= 0.474 Chirality : 0.049 0.824 1625 Planarity : 0.003 0.042 1802 Dihedral : 14.166 143.959 4006 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: -1.25 (0.24), residues: 1267 helix: 0.13 (0.22), residues: 568 sheet: -0.22 (0.42), residues: 143 loop : -2.01 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 648 HIS 0.008 0.001 HIS B 363 PHE 0.027 0.002 PHE A1437 TYR 0.022 0.002 TYR B 79 ARG 0.019 0.001 ARG A1130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 MET cc_start: -0.0507 (tmm) cc_final: -0.0782 (tmm) REVERT: A 784 PHE cc_start: 0.8947 (p90) cc_final: 0.8497 (t80) REVERT: A 1130 ARG cc_start: 0.9604 (ptp90) cc_final: 0.9308 (ptp90) REVERT: A 1200 MET cc_start: 0.9229 (mpp) cc_final: 0.8903 (mpp) REVERT: A 1213 THR cc_start: 0.8914 (m) cc_final: 0.8662 (t) REVERT: A 1421 TYR cc_start: 0.7916 (t80) cc_final: 0.7499 (t80) REVERT: A 1457 MET cc_start: 0.9097 (ppp) cc_final: 0.8592 (ppp) REVERT: B 179 LEU cc_start: 0.8636 (mp) cc_final: 0.8370 (mp) REVERT: B 182 PHE cc_start: 0.8497 (t80) cc_final: 0.7809 (t80) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2083 time to fit residues: 63.9163 Evaluate side-chains 171 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.0470 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 overall best weight: 2.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.104891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.080355 restraints weight = 41952.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.083005 restraints weight = 25309.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.084952 restraints weight = 17887.779| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10586 Z= 0.234 Angle : 0.648 13.168 14363 Z= 0.325 Chirality : 0.044 0.165 1625 Planarity : 0.004 0.039 1802 Dihedral : 8.453 127.492 1606 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.24), residues: 1267 helix: 0.09 (0.22), residues: 582 sheet: -0.26 (0.42), residues: 142 loop : -1.97 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 648 HIS 0.004 0.001 HIS A1104 PHE 0.017 0.002 PHE A1330 TYR 0.017 0.002 TYR A 678 ARG 0.006 0.001 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 MET cc_start: -0.0266 (tmm) cc_final: -0.0505 (tmm) REVERT: A 784 PHE cc_start: 0.8986 (p90) cc_final: 0.8517 (t80) REVERT: A 791 PHE cc_start: 0.8230 (t80) cc_final: 0.7998 (t80) REVERT: A 1238 ASN cc_start: 0.8563 (t0) cc_final: 0.8219 (t0) REVERT: A 1303 ILE cc_start: 0.9330 (mm) cc_final: 0.9068 (mt) REVERT: A 1341 VAL cc_start: 0.7776 (m) cc_final: 0.7571 (p) REVERT: A 1457 MET cc_start: 0.9085 (ppp) cc_final: 0.8811 (ppp) REVERT: B 169 MET cc_start: 0.8966 (mmp) cc_final: 0.8698 (tpp) REVERT: B 182 PHE cc_start: 0.8704 (t80) cc_final: 0.8047 (t80) REVERT: B 304 ASP cc_start: 0.7237 (t0) cc_final: 0.7018 (t0) REVERT: B 333 ASP cc_start: 0.8575 (m-30) cc_final: 0.8312 (m-30) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.2066 time to fit residues: 60.7432 Evaluate side-chains 170 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 104 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 0.0270 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 76 optimal weight: 0.2980 chunk 20 optimal weight: 7.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 942 HIS ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.107860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.083268 restraints weight = 41917.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.086217 restraints weight = 24528.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.088188 restraints weight = 16829.550| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 10586 Z= 0.161 Angle : 0.615 9.702 14363 Z= 0.308 Chirality : 0.044 0.155 1625 Planarity : 0.004 0.037 1802 Dihedral : 7.763 121.579 1606 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % 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: -1.18 (0.24), residues: 1267 helix: 0.09 (0.22), residues: 580 sheet: -0.06 (0.43), residues: 135 loop : -1.92 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1308 HIS 0.004 0.001 HIS A 942 PHE 0.031 0.002 PHE A1426 TYR 0.018 0.001 TYR A 678 ARG 0.003 0.000 ARG A1130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 MET cc_start: -0.0151 (tmm) cc_final: -0.0474 (tmm) REVERT: A 784 PHE cc_start: 0.8997 (p90) cc_final: 0.8539 (t80) REVERT: A 1136 LEU cc_start: 0.9496 (pp) cc_final: 0.9289 (tp) REVERT: A 1199 VAL cc_start: 0.8753 (m) cc_final: 0.8455 (m) REVERT: A 1238 ASN cc_start: 0.8494 (t0) cc_final: 0.8161 (t0) REVERT: A 1303 ILE cc_start: 0.9310 (mm) cc_final: 0.9015 (mt) REVERT: A 1317 MET cc_start: 0.8073 (ttt) cc_final: 0.7808 (tmm) REVERT: A 1457 MET cc_start: 0.9002 (ppp) cc_final: 0.8747 (ppp) REVERT: B 111 MET cc_start: 0.8827 (ppp) cc_final: 0.8289 (ppp) REVERT: B 180 GLU cc_start: 0.8121 (tp30) cc_final: 0.7486 (tm-30) REVERT: B 181 LYS cc_start: 0.8874 (tmmt) cc_final: 0.8490 (tmtt) REVERT: B 182 PHE cc_start: 0.8684 (t80) cc_final: 0.8025 (t80) REVERT: B 304 ASP cc_start: 0.7297 (t0) cc_final: 0.7012 (t0) REVERT: B 333 ASP cc_start: 0.8407 (m-30) cc_final: 0.8152 (m-30) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1955 time to fit residues: 60.2210 Evaluate side-chains 168 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 120 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.107098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.082637 restraints weight = 41431.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.085502 restraints weight = 24568.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.087551 restraints weight = 17011.893| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10586 Z= 0.157 Angle : 0.590 9.741 14363 Z= 0.297 Chirality : 0.043 0.149 1625 Planarity : 0.003 0.036 1802 Dihedral : 7.213 115.203 1606 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % 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: -1.14 (0.24), residues: 1267 helix: 0.13 (0.22), residues: 583 sheet: -0.26 (0.42), residues: 142 loop : -1.86 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1308 HIS 0.003 0.001 HIS B 363 PHE 0.021 0.001 PHE A1437 TYR 0.026 0.001 TYR B 278 ARG 0.004 0.000 ARG A 925 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 PHE cc_start: 0.7327 (t80) cc_final: 0.7087 (t80) REVERT: A 771 MET cc_start: 0.0155 (tmm) cc_final: -0.0163 (tmm) REVERT: A 784 PHE cc_start: 0.8987 (p90) cc_final: 0.8512 (t80) REVERT: A 1136 LEU cc_start: 0.9485 (pp) cc_final: 0.9279 (tp) REVERT: A 1199 VAL cc_start: 0.8708 (m) cc_final: 0.8404 (m) REVERT: A 1238 ASN cc_start: 0.8490 (t0) cc_final: 0.8142 (t0) REVERT: A 1300 ARG cc_start: 0.8619 (mpt180) cc_final: 0.8356 (mmt-90) REVERT: A 1317 MET cc_start: 0.8085 (ttt) cc_final: 0.7831 (tmm) REVERT: A 1457 MET cc_start: 0.8938 (ppp) cc_final: 0.8689 (ppp) REVERT: B 180 GLU cc_start: 0.8171 (tp30) cc_final: 0.7539 (tm-30) REVERT: B 181 LYS cc_start: 0.8821 (tmmt) cc_final: 0.8184 (tmmt) REVERT: B 182 PHE cc_start: 0.8721 (t80) cc_final: 0.8066 (t80) REVERT: B 304 ASP cc_start: 0.7353 (t0) cc_final: 0.7030 (t0) REVERT: B 333 ASP cc_start: 0.8428 (m-30) cc_final: 0.8172 (m-30) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1938 time to fit residues: 60.1870 Evaluate side-chains 172 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1041 ASN ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.105713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.081329 restraints weight = 41190.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.084146 restraints weight = 24408.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.086102 restraints weight = 16845.785| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10586 Z= 0.185 Angle : 0.613 10.122 14363 Z= 0.308 Chirality : 0.044 0.150 1625 Planarity : 0.003 0.036 1802 Dihedral : 6.931 107.798 1606 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.24), residues: 1267 helix: 0.11 (0.22), residues: 583 sheet: -0.31 (0.41), residues: 142 loop : -1.89 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1308 HIS 0.006 0.001 HIS A1350 PHE 0.017 0.001 PHE A1368 TYR 0.020 0.001 TYR A 678 ARG 0.004 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 PHE cc_start: 0.7359 (t80) cc_final: 0.7124 (t80) REVERT: A 784 PHE cc_start: 0.9012 (p90) cc_final: 0.8502 (t80) REVERT: A 1136 LEU cc_start: 0.9527 (pp) cc_final: 0.9319 (tp) REVERT: A 1199 VAL cc_start: 0.8700 (m) cc_final: 0.8391 (m) REVERT: A 1300 ARG cc_start: 0.8721 (mpt180) cc_final: 0.8470 (mmt-90) REVERT: A 1303 ILE cc_start: 0.9325 (mm) cc_final: 0.9063 (mt) REVERT: A 1317 MET cc_start: 0.8085 (ttt) cc_final: 0.7861 (tmm) REVERT: B 111 MET cc_start: 0.8848 (ppp) cc_final: 0.8354 (ppp) REVERT: B 180 GLU cc_start: 0.8250 (tp30) cc_final: 0.7475 (tm-30) REVERT: B 181 LYS cc_start: 0.8852 (tmmt) cc_final: 0.8275 (tmtt) REVERT: B 182 PHE cc_start: 0.8756 (t80) cc_final: 0.8007 (t80) REVERT: B 333 ASP cc_start: 0.8510 (m-30) cc_final: 0.8213 (m-30) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1942 time to fit residues: 58.4264 Evaluate side-chains 168 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-dev-5592/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-dev-5592/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-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-dev-5592/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-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-dev-5592/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-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.65 > 50: distance: 11 - 96: 8.009 distance: 56 - 117: 31.625 distance: 59 - 114: 23.721 distance: 68 - 100: 13.511 distance: 71 - 97: 5.487 distance: 86 - 91: 20.452 distance: 91 - 92: 24.216 distance: 91 - 248: 21.190 distance: 92 - 93: 14.739 distance: 92 - 95: 8.853 distance: 93 - 94: 13.294 distance: 94 - 245: 12.370 distance: 95 - 96: 16.035 distance: 97 - 98: 7.581 distance: 98 - 99: 8.460 distance: 98 - 101: 16.760 distance: 99 - 100: 13.445 distance: 99 - 106: 15.019 distance: 101 - 102: 11.541 distance: 102 - 103: 12.411 distance: 103 - 104: 5.472 distance: 103 - 105: 11.104 distance: 106 - 107: 34.395 distance: 106 - 236: 18.710 distance: 107 - 108: 33.679 distance: 107 - 110: 15.337 distance: 108 - 109: 46.288 distance: 108 - 114: 12.444 distance: 109 - 233: 23.674 distance: 110 - 111: 30.601 distance: 110 - 112: 22.422 distance: 111 - 113: 18.502 distance: 114 - 115: 8.966 distance: 115 - 116: 46.652 distance: 115 - 118: 30.887 distance: 116 - 117: 18.626 distance: 116 - 125: 17.859 distance: 118 - 119: 46.330 distance: 119 - 120: 25.327 distance: 120 - 121: 3.780 distance: 121 - 122: 10.591 distance: 122 - 123: 9.232 distance: 122 - 124: 9.912 distance: 125 - 126: 35.592 distance: 125 - 217: 27.966 distance: 126 - 127: 56.137 distance: 126 - 129: 20.704 distance: 127 - 128: 26.701 distance: 127 - 136: 15.039 distance: 128 - 214: 12.757 distance: 129 - 130: 34.998 distance: 130 - 131: 31.292 distance: 130 - 132: 28.185 distance: 131 - 133: 31.706 distance: 132 - 134: 9.544 distance: 133 - 135: 12.706 distance: 134 - 135: 16.153 distance: 136 - 137: 22.369 distance: 137 - 138: 23.507 distance: 137 - 140: 19.965 distance: 138 - 139: 42.582 distance: 138 - 143: 21.355 distance: 140 - 141: 12.830 distance: 140 - 142: 18.005 distance: 143 - 144: 25.304 distance: 143 - 204: 13.116 distance: 144 - 145: 33.708 distance: 144 - 147: 7.211 distance: 145 - 146: 24.107 distance: 145 - 150: 36.530 distance: 146 - 201: 20.345 distance: 147 - 148: 27.472 distance: 147 - 149: 23.779 distance: 150 - 151: 24.477 distance: 150 - 156: 25.081 distance: 151 - 152: 39.238 distance: 151 - 154: 32.676 distance: 152 - 153: 21.957 distance: 152 - 157: 18.896 distance: 154 - 155: 21.661 distance: 155 - 156: 18.703 distance: 157 - 158: 20.110 distance: 158 - 159: 10.701 distance: 158 - 161: 20.581 distance: 159 - 160: 32.290 distance: 159 - 163: 27.061 distance: 161 - 162: 24.024 distance: 163 - 164: 13.862 distance: 164 - 165: 4.383 distance: 164 - 167: 4.781 distance: 165 - 166: 10.709 distance: 165 - 171: 6.712 distance: 167 - 168: 16.430 distance: 168 - 169: 12.158 distance: 168 - 170: 13.429