Starting phenix.real_space_refine on Thu Apr 11 07:17:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rf0_19114/04_2024/8rf0_19114_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rf0_19114/04_2024/8rf0_19114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rf0_19114/04_2024/8rf0_19114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rf0_19114/04_2024/8rf0_19114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rf0_19114/04_2024/8rf0_19114_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rf0_19114/04_2024/8rf0_19114_updated.pdb" } resolution = 3.4 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= 0.019 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 70 5.16 5 C 13815 2.51 5 N 3881 2.21 5 O 4154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 66": "OE1" <-> "OE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 692": "OD1" <-> "OD2" Residue "A TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2146": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 21922 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 21699 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2780, 21677 Classifications: {'peptide': 2780} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 114, 'TRANS': 2665} Chain breaks: 4 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 9, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 158 Conformer: "B" Number of residues, atoms: 2780, 21677 Classifications: {'peptide': 2780} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 114, 'TRANS': 2665} Chain breaks: 4 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 9, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 158 bond proxies already assigned to first conformer: 22150 Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 99 Unusual residues: {'BGC': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 99 Unusual residues: {'BGC': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UPG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 194 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG A 194 " occ=0.40 residue: pdb=" N AARG A1355 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A1355 " occ=0.50 Time building chain proxies: 20.78, per 1000 atoms: 0.95 Number of scatterers: 21922 At special positions: 0 Unit cell: (102.648, 122.388, 213.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 2 15.00 O 4154 8.00 N 3881 7.00 C 13815 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 Links applied BETA1-2 " BGC B 1 " - " BGC B 2 " " BGC B 2 " - " BGC B 3 " " BGC B 3 " - " BGC B 4 " " BGC B 4 " - " BGC B 5 " " BGC B 5 " - " BGC B 6 " " BGC B 6 " - " BGC B 7 " " BGC B 7 " - " BGC B 8 " " BGC B 8 " - " BGC B 9 " " BGC C 2 " - " BGC C 3 " " BGC C 3 " - " BGC C 4 " " BGC C 5 " - " BGC C 6 " " BGC C 6 " - " BGC C 7 " " BGC C 7 " - " BGC C 8 " " BGC C 8 " - " BGC C 9 " BETA1-3 " BGC C 1 " - " BGC C 2 " " BGC C 4 " - " BGC C 5 " Time building additional restraints: 8.49 Conformation dependent library (CDL) restraints added in 7.6 seconds 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5172 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 17 sheets defined 40.9% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.66 Creating SS restraints... Processing helix chain 'A' and resid 35 through 44 removed outlier: 3.754A pdb=" N ARG A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 78 removed outlier: 3.971A pdb=" N TYR A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N THR A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 95 removed outlier: 4.074A pdb=" N TRP A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 104 Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.739A pdb=" N GLN A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 141 removed outlier: 3.597A pdb=" N GLY A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP A 137 " --> pdb=" O MET A 133 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 141 " --> pdb=" O TRP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 161 removed outlier: 4.170A pdb=" N THR A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 211 removed outlier: 4.182A pdb=" N ARG A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASN A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.887A pdb=" N GLN A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N SER A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 243 removed outlier: 3.525A pdb=" N TYR A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 268 through 275 removed outlier: 3.783A pdb=" N HIS A 275 " --> pdb=" O MET A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 297 removed outlier: 3.533A pdb=" N VAL A 289 " --> pdb=" O MET A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 310 through 315 removed outlier: 3.692A pdb=" N LEU A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 322 No H-bonds generated for 'chain 'A' and resid 320 through 322' Processing helix chain 'A' and resid 325 through 341 removed outlier: 3.519A pdb=" N ARG A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 360 removed outlier: 3.543A pdb=" N ALA A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP A 360 " --> pdb=" O MET A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 382 through 389 Processing helix chain 'A' and resid 395 through 406 Processing helix chain 'A' and resid 408 through 429 removed outlier: 4.650A pdb=" N ALA A 413 " --> pdb=" O ALA A 410 " (cutoff:3.500A) Proline residue: A 414 - end of helix Processing helix chain 'A' and resid 440 through 466 removed outlier: 4.421A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 500 through 514 Processing helix chain 'A' and resid 539 through 556 removed outlier: 3.607A pdb=" N ARG A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.503A pdb=" N LEU A 597 " --> pdb=" O GLU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 642 removed outlier: 3.661A pdb=" N GLY A 639 " --> pdb=" O THR A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 646 No H-bonds generated for 'chain 'A' and resid 644 through 646' Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 703 through 706 No H-bonds generated for 'chain 'A' and resid 703 through 706' Processing helix chain 'A' and resid 719 through 729 removed outlier: 3.993A pdb=" N ARG A 729 " --> pdb=" O ALA A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 745 Processing helix chain 'A' and resid 767 through 786 removed outlier: 3.719A pdb=" N LEU A 782 " --> pdb=" O ASP A 778 " (cutoff:3.500A) Proline residue: A 783 - end of helix Processing helix chain 'A' and resid 794 through 823 Proline residue: A 810 - end of helix removed outlier: 3.599A pdb=" N TYR A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 851 removed outlier: 3.750A pdb=" N GLN A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 840 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Proline residue: A 844 - end of helix removed outlier: 5.343A pdb=" N SER A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 848 " --> pdb=" O PRO A 844 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 905 removed outlier: 5.210A pdb=" N ALA A 887 " --> pdb=" O ILE A 883 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP A 888 " --> pdb=" O VAL A 884 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 903 " --> pdb=" O ARG A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 935 removed outlier: 3.553A pdb=" N TYR A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG A 933 " --> pdb=" O VAL A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 951 removed outlier: 4.082A pdb=" N LEU A 951 " --> pdb=" O LEU A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 978 Proline residue: A 962 - end of helix removed outlier: 4.292A pdb=" N SER A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) Proline residue: A 971 - end of helix Processing helix chain 'A' and resid 992 through 1010 removed outlier: 3.814A pdb=" N ARG A1006 " --> pdb=" O ARG A1002 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR A1007 " --> pdb=" O ARG A1003 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TYR A1008 " --> pdb=" O THR A1004 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A1009 " --> pdb=" O TRP A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1054 Processing helix chain 'A' and resid 1059 through 1075 removed outlier: 3.595A pdb=" N LEU A1063 " --> pdb=" O PHE A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1124 removed outlier: 3.549A pdb=" N ALA A1114 " --> pdb=" O GLY A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1150 removed outlier: 3.640A pdb=" N ALA A1141 " --> pdb=" O ILE A1137 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A1150 " --> pdb=" O GLU A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1181 Processing helix chain 'A' and resid 1187 through 1210 removed outlier: 3.649A pdb=" N ASN A1192 " --> pdb=" O ILE A1188 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A1193 " --> pdb=" O ARG A1189 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A1194 " --> pdb=" O VAL A1190 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A1196 " --> pdb=" O ASN A1192 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A1210 " --> pdb=" O ASN A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1238 Processing helix chain 'A' and resid 1245 through 1262 removed outlier: 3.696A pdb=" N LEU A1261 " --> pdb=" O ARG A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1287 No H-bonds generated for 'chain 'A' and resid 1285 through 1287' Processing helix chain 'A' and resid 1300 through 1311 removed outlier: 3.807A pdb=" N LEU A1303 " --> pdb=" O GLU A1300 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A1305 " --> pdb=" O ARG A1302 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A1311 " --> pdb=" O ALA A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1319 No H-bonds generated for 'chain 'A' and resid 1316 through 1319' Processing helix chain 'A' and resid 1342 through 1351 removed outlier: 4.145A pdb=" N LEU A1346 " --> pdb=" O PHE A1343 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N MET A1347 " --> pdb=" O GLU A1344 " (cutoff:3.500A) Proline residue: A1348 - end of helix Processing helix chain 'A' and resid 1359 through 1378 Processing helix chain 'A' and resid 1422 through 1427 removed outlier: 3.988A pdb=" N ILE A1426 " --> pdb=" O PRO A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1445 Processing helix chain 'A' and resid 1483 through 1493 Processing helix chain 'A' and resid 1497 through 1504 removed outlier: 3.624A pdb=" N HIS A1503 " --> pdb=" O ARG A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1510 Processing helix chain 'A' and resid 1512 through 1514 No H-bonds generated for 'chain 'A' and resid 1512 through 1514' Processing helix chain 'A' and resid 1553 through 1555 No H-bonds generated for 'chain 'A' and resid 1553 through 1555' Processing helix chain 'A' and resid 1692 through 1695 No H-bonds generated for 'chain 'A' and resid 1692 through 1695' Processing helix chain 'A' and resid 1697 through 1702 Processing helix chain 'A' and resid 1751 through 1755 Processing helix chain 'A' and resid 1811 through 1821 removed outlier: 3.734A pdb=" N ASP A1815 " --> pdb=" O ARG A1811 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A1816 " --> pdb=" O GLU A1812 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A1819 " --> pdb=" O ASP A1815 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ARG A1820 " --> pdb=" O LYS A1816 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A1821 " --> pdb=" O ALA A1817 " (cutoff:3.500A) Processing helix chain 'A' and resid 1831 through 1844 Processing helix chain 'A' and resid 1849 through 1863 Processing helix chain 'A' and resid 1886 through 1888 No H-bonds generated for 'chain 'A' and resid 1886 through 1888' Processing helix chain 'A' and resid 1910 through 1924 removed outlier: 3.641A pdb=" N ARG A1924 " --> pdb=" O TYR A1920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1956 removed outlier: 4.542A pdb=" N GLN A1942 " --> pdb=" O ALA A1938 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASP A1943 " --> pdb=" O SER A1939 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A1951 " --> pdb=" O ALA A1947 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N THR A1954 " --> pdb=" O HIS A1950 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLN A1955 " --> pdb=" O ILE A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1987 Processing helix chain 'A' and resid 2002 through 2010 removed outlier: 3.676A pdb=" N VAL A2007 " --> pdb=" O ILE A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2025 through 2027 No H-bonds generated for 'chain 'A' and resid 2025 through 2027' Processing helix chain 'A' and resid 2213 through 2215 No H-bonds generated for 'chain 'A' and resid 2213 through 2215' Processing helix chain 'A' and resid 2257 through 2260 No H-bonds generated for 'chain 'A' and resid 2257 through 2260' Processing helix chain 'A' and resid 2317 through 2330 removed outlier: 3.605A pdb=" N GLN A2329 " --> pdb=" O LYS A2325 " (cutoff:3.500A) Processing helix chain 'A' and resid 2333 through 2347 Processing helix chain 'A' and resid 2359 through 2363 Processing helix chain 'A' and resid 2366 through 2375 Processing helix chain 'A' and resid 2391 through 2395 removed outlier: 3.679A pdb=" N LEU A2395 " --> pdb=" O PHE A2391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2391 through 2395' Processing helix chain 'A' and resid 2398 through 2400 No H-bonds generated for 'chain 'A' and resid 2398 through 2400' Processing helix chain 'A' and resid 2407 through 2419 removed outlier: 3.633A pdb=" N GLY A2418 " --> pdb=" O LEU A2414 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG A2419 " --> pdb=" O ARG A2415 " (cutoff:3.500A) Processing helix chain 'A' and resid 2445 through 2459 removed outlier: 4.287A pdb=" N LEU A2449 " --> pdb=" O ASP A2445 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA A2450 " --> pdb=" O VAL A2446 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A2451 " --> pdb=" O VAL A2447 " (cutoff:3.500A) Processing helix chain 'A' and resid 2463 through 2465 No H-bonds generated for 'chain 'A' and resid 2463 through 2465' Processing helix chain 'A' and resid 2498 through 2511 removed outlier: 3.676A pdb=" N ALA A2505 " --> pdb=" O HIS A2501 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2561 removed outlier: 3.940A pdb=" N ASP A2554 " --> pdb=" O GLY A2550 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU A2557 " --> pdb=" O ARG A2553 " (cutoff:3.500A) Processing helix chain 'A' and resid 2565 through 2584 removed outlier: 3.676A pdb=" N LYS A2570 " --> pdb=" O ASP A2566 " (cutoff:3.500A) Processing helix chain 'A' and resid 2615 through 2624 removed outlier: 3.945A pdb=" N VAL A2622 " --> pdb=" O GLN A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2629 through 2643 removed outlier: 3.856A pdb=" N MET A2640 " --> pdb=" O MET A2636 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU A2641 " --> pdb=" O ASP A2637 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N HIS A2642 " --> pdb=" O ALA A2638 " (cutoff:3.500A) Processing helix chain 'A' and resid 2667 through 2670 Processing helix chain 'A' and resid 2683 through 2696 removed outlier: 4.284A pdb=" N TRP A2688 " --> pdb=" O HIS A2684 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL A2689 " --> pdb=" O ALA A2685 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A2690 " --> pdb=" O ALA A2686 " (cutoff:3.500A) Processing helix chain 'A' and resid 2699 through 2709 Processing helix chain 'A' and resid 2754 through 2763 Processing sheet with id= A, first strand: chain 'A' and resid 716 through 718 removed outlier: 4.247A pdb=" N TYR A 717 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL A 620 " --> pdb=" O TYR A 717 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 491 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 524 " --> pdb=" O TYR A 566 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 526 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1099 through 1101 Processing sheet with id= C, first strand: chain 'A' and resid 1326 through 1328 removed outlier: 3.586A pdb=" N ALA A1334 " --> pdb=" O VAL A1327 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1457 through 1459 removed outlier: 4.472A pdb=" N ALA A1457 " --> pdb=" O VAL A1474 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1561 through 1564 removed outlier: 3.595A pdb=" N MET A1571 " --> pdb=" O TYR A1579 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1613 through 1615 removed outlier: 3.831A pdb=" N VAL A1793 " --> pdb=" O ARG A1675 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A1677 " --> pdb=" O VAL A1791 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1627 through 1631 removed outlier: 3.878A pdb=" N LYS A1627 " --> pdb=" O THR A1642 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A1642 " --> pdb=" O LYS A1627 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN A1647 " --> pdb=" O LEU A1668 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A1668 " --> pdb=" O GLN A1647 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A1799 " --> pdb=" O LEU A1667 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP A1804 " --> pdb=" O LEU A1734 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1990 through 1993 removed outlier: 3.916A pdb=" N LEU A1992 " --> pdb=" O SER A1899 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A1902 " --> pdb=" O VAL A1933 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 2051 through 2053 removed outlier: 3.530A pdb=" N VAL A2061 " --> pdb=" O GLY A2052 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A2060 " --> pdb=" O HIS A2150 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A2146 " --> pdb=" O LEU A2064 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A2312 " --> pdb=" O PHE A2243 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA A2226 " --> pdb=" O ASP A2221 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 2075 through 2080 removed outlier: 3.770A pdb=" N PHE A2083 " --> pdb=" O ASN A2080 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 2120 through 2122 Processing sheet with id= L, first strand: chain 'A' and resid 2184 through 2186 removed outlier: 3.736A pdb=" N VAL A2185 " --> pdb=" O ARG A2305 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A2305 " --> pdb=" O VAL A2185 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'A' and resid 2193 through 2197 removed outlier: 3.575A pdb=" N ARG A2193 " --> pdb=" O LEU A2299 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A2197 " --> pdb=" O GLN A2295 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN A2295 " --> pdb=" O VAL A2197 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 2350 through 2352 removed outlier: 3.606A pdb=" N PHE A2788 " --> pdb=" O VAL A2803 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 2388 through 2390 removed outlier: 3.710A pdb=" N TRP A2430 " --> pdb=" O PHE A2389 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 2472 through 2474 removed outlier: 3.942A pdb=" N PHE A2472 " --> pdb=" O SER A2492 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 2768 through 2770 removed outlier: 3.514A pdb=" N THR A2769 " --> pdb=" O HIS A2776 " (cutoff:3.500A) 798 hydrogen bonds defined for protein. 2248 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: 11.03 Time building geometry restraints manager: 9.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3636 1.31 - 1.44: 6283 1.44 - 1.56: 12373 1.56 - 1.69: 5 1.69 - 1.82: 125 Bond restraints: 22422 Sorted by residual: bond pdb=" O3B UPG A2901 " pdb=" PB UPG A2901 " ideal model delta sigma weight residual 1.652 1.490 0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" C PRO A1520 " pdb=" N ARG A1521 " ideal model delta sigma weight residual 1.330 1.434 -0.103 1.38e-02 5.25e+03 5.61e+01 bond pdb=" C ALA A1519 " pdb=" N PRO A1520 " ideal model delta sigma weight residual 1.334 1.472 -0.138 2.34e-02 1.83e+03 3.46e+01 bond pdb=" O1B UPG A2901 " pdb=" PB UPG A2901 " ideal model delta sigma weight residual 1.493 1.600 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" CA PRO A1520 " pdb=" C PRO A1520 " ideal model delta sigma weight residual 1.520 1.593 -0.073 1.42e-02 4.96e+03 2.65e+01 ... (remaining 22417 not shown) Histogram of bond angle deviations from ideal: 82.30 - 92.68: 1 92.68 - 103.07: 166 103.07 - 113.45: 12597 113.45 - 123.83: 16933 123.83 - 134.21: 776 Bond angle restraints: 30473 Sorted by residual: angle pdb=" O ALA A1519 " pdb=" C ALA A1519 " pdb=" N PRO A1520 " ideal model delta sigma weight residual 121.32 82.30 39.02 1.15e+00 7.56e-01 1.15e+03 angle pdb=" N PRO A2030 " pdb=" CA PRO A2030 " pdb=" CB PRO A2030 " ideal model delta sigma weight residual 102.81 109.81 -7.00 6.70e-01 2.23e+00 1.09e+02 angle pdb=" CA PRO A1520 " pdb=" C PRO A1520 " pdb=" O PRO A1520 " ideal model delta sigma weight residual 120.60 107.12 13.48 1.82e+00 3.02e-01 5.48e+01 angle pdb=" N PRO A2037 " pdb=" CA PRO A2037 " pdb=" CB PRO A2037 " ideal model delta sigma weight residual 103.25 110.79 -7.54 1.05e+00 9.07e-01 5.16e+01 angle pdb=" N PRO A2028 " pdb=" CA PRO A2028 " pdb=" CB PRO A2028 " ideal model delta sigma weight residual 103.25 110.77 -7.52 1.05e+00 9.07e-01 5.13e+01 ... (remaining 30468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 12553 23.68 - 47.37: 793 47.37 - 71.05: 83 71.05 - 94.73: 43 94.73 - 118.42: 41 Dihedral angle restraints: 13513 sinusoidal: 5478 harmonic: 8035 Sorted by residual: dihedral pdb=" CA TYR A 139 " pdb=" C TYR A 139 " pdb=" N VAL A 140 " pdb=" CA VAL A 140 " ideal model delta harmonic sigma weight residual 180.00 146.39 33.61 0 5.00e+00 4.00e-02 4.52e+01 dihedral pdb=" N PRO A1520 " pdb=" C PRO A1520 " pdb=" CA PRO A1520 " pdb=" CB PRO A1520 " ideal model delta harmonic sigma weight residual 115.10 127.06 -11.96 0 2.50e+00 1.60e-01 2.29e+01 dihedral pdb=" CA GLN A1015 " pdb=" C GLN A1015 " pdb=" N GLU A1016 " pdb=" CA GLU A1016 " ideal model delta harmonic sigma weight residual 180.00 -156.89 -23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 13510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3082 0.074 - 0.148: 293 0.148 - 0.222: 18 0.222 - 0.296: 11 0.296 - 0.370: 2 Chirality restraints: 3406 Sorted by residual: chirality pdb=" C1 BGC B 2 " pdb=" O2 BGC B 1 " pdb=" C2 BGC B 2 " pdb=" O5 BGC B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.57e+02 chirality pdb=" C1 BGC B 3 " pdb=" O2 BGC B 2 " pdb=" C2 BGC B 3 " pdb=" O5 BGC B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.20e+01 chirality pdb=" C1 BGC B 7 " pdb=" O2 BGC B 6 " pdb=" C2 BGC B 7 " pdb=" O5 BGC B 7 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.43e+01 ... (remaining 3403 not shown) Planarity restraints: 3947 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A1519 " -0.141 2.00e-02 2.50e+03 2.15e-01 4.64e+02 pdb=" C ALA A1519 " 0.372 2.00e-02 2.50e+03 pdb=" O ALA A1519 " -0.137 2.00e-02 2.50e+03 pdb=" N PRO A1520 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 100 " -0.033 2.00e-02 2.50e+03 6.51e-02 4.24e+01 pdb=" C ILE A 100 " 0.113 2.00e-02 2.50e+03 pdb=" O ILE A 100 " -0.042 2.00e-02 2.50e+03 pdb=" N GLU A 101 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 585 " -0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C GLU A 585 " 0.081 2.00e-02 2.50e+03 pdb=" O GLU A 585 " -0.032 2.00e-02 2.50e+03 pdb=" N ARG A 586 " -0.027 2.00e-02 2.50e+03 ... (remaining 3944 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 795 2.72 - 3.26: 22737 3.26 - 3.81: 35412 3.81 - 4.35: 42343 4.35 - 4.90: 70838 Nonbonded interactions: 172125 Sorted by model distance: nonbonded pdb=" OG SER A1337 " pdb=" OH TYR A1345 " model vdw 2.171 2.440 nonbonded pdb=" OG1 THR A2255 " pdb=" O THR A2282 " model vdw 2.204 2.440 nonbonded pdb=" O ASN A1417 " pdb=" OG1 THR A1461 " model vdw 2.223 2.440 nonbonded pdb=" O LEU A2466 " pdb=" OG1 THR A2497 " model vdw 2.228 2.440 nonbonded pdb=" O TRP A2343 " pdb=" OG1 THR A2347 " model vdw 2.228 2.440 ... (remaining 172120 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.030 Extract box with map and model: 6.980 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 75.260 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.160 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 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 0.162 22422 Z= 0.271 Angle : 0.730 39.017 30473 Z= 0.428 Chirality : 0.045 0.370 3406 Planarity : 0.006 0.215 3947 Dihedral : 16.919 118.415 8341 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.90 % Allowed : 8.84 % Favored : 90.25 % Rotamer: Outliers : 0.45 % Allowed : 0.32 % Favored : 99.23 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.04 (0.16), residues: 2776 helix: 0.93 (0.17), residues: 1128 sheet: 0.16 (0.31), residues: 316 loop : -2.48 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A 967 HIS 0.004 0.001 HIS A 569 PHE 0.016 0.001 PHE A 238 TYR 0.012 0.001 TYR A 931 ARG 0.005 0.000 ARG A1324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 538 time to evaluate : 2.388 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: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.4396 (mt) cc_final: 0.3371 (mm) REVERT: A 232 PRO cc_start: 0.8523 (Cg_endo) cc_final: 0.8302 (Cg_exo) REVERT: A 251 PHE cc_start: 0.6085 (t80) cc_final: 0.5750 (t80) REVERT: A 356 MET cc_start: 0.7515 (ttm) cc_final: 0.7220 (tmm) REVERT: A 467 VAL cc_start: 0.7893 (t) cc_final: 0.7231 (m) REVERT: A 505 MET cc_start: 0.7514 (mmp) cc_final: 0.7264 (mmt) REVERT: A 524 LEU cc_start: 0.7879 (tt) cc_final: 0.7224 (tt) REVERT: A 582 MET cc_start: 0.6806 (ppp) cc_final: 0.6061 (ppp) REVERT: A 643 HIS cc_start: 0.7334 (t70) cc_final: 0.7054 (t70) REVERT: A 798 TRP cc_start: 0.7048 (t60) cc_final: 0.6843 (t-100) REVERT: A 800 MET cc_start: 0.4891 (mtm) cc_final: 0.4434 (tpt) REVERT: A 824 MET cc_start: 0.5377 (mtt) cc_final: 0.5115 (mmp) REVERT: A 892 MET cc_start: 0.7368 (mmp) cc_final: 0.7089 (mmp) REVERT: A 911 MET cc_start: 0.5015 (ppp) cc_final: 0.4581 (tpp) REVERT: A 931 TYR cc_start: 0.6049 (m-10) cc_final: 0.5758 (m-10) REVERT: A 1750 ASP cc_start: 0.7783 (t0) cc_final: 0.7192 (p0) REVERT: A 1782 ASP cc_start: 0.6176 (t0) cc_final: 0.5715 (t0) REVERT: A 1822 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.6398 (tpm170) REVERT: A 2105 LEU cc_start: 0.7617 (mt) cc_final: 0.7132 (mt) REVERT: A 2198 TYR cc_start: 0.4472 (m-10) cc_final: 0.4046 (m-10) REVERT: A 2273 ILE cc_start: 0.5792 (tt) cc_final: 0.5549 (tt) REVERT: A 2299 LEU cc_start: 0.6635 (mt) cc_final: 0.6407 (mt) REVERT: A 2401 PHE cc_start: 0.3035 (t80) cc_final: 0.2666 (t80) REVERT: A 2420 GLN cc_start: 0.7030 (tt0) cc_final: 0.6614 (tt0) REVERT: A 2527 ASN cc_start: 0.7327 (t160) cc_final: 0.6697 (t0) REVERT: A 2603 LEU cc_start: 0.6639 (tp) cc_final: 0.6179 (tp) REVERT: A 2684 HIS cc_start: 0.7282 (t-170) cc_final: 0.7072 (t-90) REVERT: A 2712 VAL cc_start: 0.5730 (t) cc_final: 0.5389 (t) outliers start: 6 outliers final: 3 residues processed: 543 average time/residue: 0.4613 time to fit residues: 361.6411 Evaluate side-chains 257 residues out of total 2299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 254 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 1327 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 217 optimal weight: 0.0170 chunk 84 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 162 optimal weight: 0.4980 chunk 252 optimal weight: 0.0050 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 ASN ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 GLN A1111 HIS A1362 GLN A1480 HIS ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1720 ASN ** A1823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 HIS ** A2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2428 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22422 Z= 0.194 Angle : 0.694 14.411 30473 Z= 0.344 Chirality : 0.044 0.211 3406 Planarity : 0.006 0.135 3947 Dihedral : 12.426 113.965 3452 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.99 % Favored : 90.40 % Rotamer: Outliers : 1.62 % Allowed : 10.53 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.16 (0.16), residues: 2776 helix: 0.71 (0.16), residues: 1160 sheet: 0.27 (0.30), residues: 323 loop : -2.55 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A2785 HIS 0.013 0.001 HIS A1823 PHE 0.028 0.002 PHE A2359 TYR 0.034 0.001 TYR A 139 ARG 0.010 0.001 ARG A1248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5552 Ramachandran restraints generated. 2776 Oldfield, 0 Emsley, 2776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 265 time to evaluate : 2.903 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.4240 (mt) cc_final: 0.3492 (mm) REVERT: A 290 LYS cc_start: 0.9015 (mttp) cc_final: 0.8617 (mptt) REVERT: A 403 MET cc_start: 0.7735 (mtt) cc_final: 0.7097 (ptt) REVERT: A 428 TRP cc_start: 0.6095 (t-100) cc_final: 0.5876 (t60) REVERT: A 505 MET cc_start: 0.7420 (mmp) cc_final: 0.7091 (mmt) REVERT: A 598 LEU cc_start: 0.8466 (mt) cc_final: 0.8202 (mt) REVERT: A 643 HIS cc_start: 0.7512 (t70) cc_final: 0.7147 (t70) REVERT: A 903 ARG cc_start: 0.3594 (mpt-90) cc_final: 0.3380 (mpt180) REVERT: A 911 MET cc_start: 0.5192 (ppp) cc_final: 0.4914 (tpp) REVERT: A 931 TYR cc_start: 0.6064 (m-10) cc_final: 0.5592 (m-10) REVERT: A 1153 ASP cc_start: 0.3904 (m-30) cc_final: 0.3005 (m-30) REVERT: A 1398 TYR cc_start: 0.7271 (m-80) cc_final: 0.7044 (m-80) REVERT: A 1822 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.6490 (tpm170) REVERT: A 2105 LEU cc_start: 0.7297 (mt) cc_final: 0.7091 (mt) REVERT: A 2158 THR cc_start: 0.6650 (m) cc_final: 0.5946 (t) REVERT: A 2401 PHE cc_start: 0.2834 (t80) cc_final: 0.2586 (t80) REVERT: A 2420 GLN cc_start: 0.7079 (tt0) cc_final: 0.6702 (tt0) outliers start: 32 outliers final: 25 residues processed: 286 average time/residue: 0.4037 time to fit residues: 180.0689 Evaluate side-chains 238 residues out of total 2299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 213 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1362 GLN Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1501 LEU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 2075 ILE Chi-restraints excluded: chain A residue 2082 ASN Chi-restraints excluded: chain A residue 2145 MET Chi-restraints excluded: chain A residue 2335 VAL Chi-restraints excluded: chain A residue 2354 THR Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 2578 LEU Chi-restraints excluded: chain A residue 2691 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-dev-5288/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-dev-5288/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: 50.306 > 50: distance: 147 - 148: 5.526 distance: 148 - 149: 4.375 distance: 148 - 151: 9.406 distance: 149 - 150: 6.137 distance: 151 - 152: 9.396 distance: 152 - 153: 7.879 distance: 153 - 154: 8.412 distance: 153 - 155: 3.095 distance: 156 - 157: 5.250 distance: 157 - 158: 4.366 distance: 157 - 160: 4.858 distance: 158 - 159: 8.742 distance: 158 - 163: 8.229 distance: 160 - 161: 6.022 distance: 160 - 162: 7.196 distance: 163 - 164: 4.181 distance: 164 - 167: 7.794 distance: 165 - 171: 8.243 distance: 167 - 168: 13.915 distance: 168 - 169: 12.246 distance: 168 - 170: 8.371 distance: 171 - 172: 6.260 distance: 172 - 173: 9.183 distance: 173 - 174: 7.508 distance: 173 - 175: 6.548 distance: 176 - 179: 3.199 distance: 177 - 178: 3.306 distance: 179 - 180: 5.763 distance: 180 - 181: 11.296 distance: 180 - 182: 4.747 distance: 183 - 184: 6.320 distance: 183 - 189: 5.286 distance: 184 - 185: 6.482 distance: 184 - 187: 9.769 distance: 185 - 186: 3.184 distance: 185 - 190: 4.920 distance: 187 - 188: 8.018 distance: 188 - 189: 6.811 distance: 190 - 191: 8.084 distance: 191 - 192: 8.912 distance: 191 - 194: 14.937 distance: 192 - 193: 15.961 distance: 192 - 196: 12.150 distance: 194 - 195: 27.351 distance: 196 - 197: 8.601 distance: 197 - 198: 17.477 distance: 197 - 200: 19.479 distance: 198 - 199: 7.450 distance: 198 - 201: 4.715 distance: 201 - 202: 5.410 distance: 202 - 203: 21.305 distance: 202 - 205: 10.410 distance: 203 - 204: 21.895 distance: 203 - 206: 10.876 distance: 206 - 207: 3.999 distance: 207 - 208: 16.454 distance: 207 - 210: 11.263 distance: 208 - 209: 18.205 distance: 208 - 214: 10.143 distance: 210 - 211: 13.932 distance: 211 - 212: 9.550 distance: 211 - 213: 14.852