Starting phenix.real_space_refine on Thu Jul 25 17:49:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/07_2024/7peb_13351.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/07_2024/7peb_13351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/07_2024/7peb_13351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/07_2024/7peb_13351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/07_2024/7peb_13351.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peb_13351/07_2024/7peb_13351.cif" } resolution = 3.67 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= 0.013 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 6 5.49 5 S 193 5.16 5 C 18556 2.51 5 N 5084 2.21 5 O 5301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 29140 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1862 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain breaks: 7 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'UNK:plan-1': 31} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 15606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1949, 15606 Classifications: {'peptide': 1949} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 80, 'TRANS': 1868} Chain breaks: 12 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'UNK:plan-1': 25} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2456 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "E" Number of atoms: 8385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8385 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 5 Chain: "I" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.49, per 1000 atoms: 0.60 Number of scatterers: 29140 At special positions: 0 Unit cell: (247.976, 169.024, 152.344, 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 193 16.00 P 6 15.00 O 5301 8.00 N 5084 7.00 C 18556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.17 Conformation dependent library (CDL) restraints added in 5.2 seconds 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6992 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 24 sheets defined 65.0% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 18 through 30 Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.789A pdb=" N UNK A 52 " --> pdb=" O UNK A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.938A pdb=" N LEU A 74 " --> pdb=" O HIS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 removed outlier: 3.600A pdb=" N SER A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 4.216A pdb=" N ASN A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 135 Processing helix chain 'A' and resid 140 through 156 Processing helix chain 'A' and resid 164 through 179 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 187 through 198 removed outlier: 3.731A pdb=" N VAL A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.683A pdb=" N VAL A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 261 through 276 removed outlier: 3.632A pdb=" N LEU A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 289 removed outlier: 4.290A pdb=" N GLU A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 No H-bonds generated for 'chain 'A' and resid 361 through 368' Processing helix chain 'A' and resid 371 through 376 No H-bonds generated for 'chain 'A' and resid 371 through 376' Processing helix chain 'A' and resid 387 through 404 No H-bonds generated for 'chain 'A' and resid 387 through 404' Processing helix chain 'A' and resid 411 through 426 No H-bonds generated for 'chain 'A' and resid 411 through 426' Processing helix chain 'A' and resid 429 through 444 No H-bonds generated for 'chain 'A' and resid 429 through 444' Processing helix chain 'A' and resid 446 through 450 No H-bonds generated for 'chain 'A' and resid 446 through 450' Processing helix chain 'A' and resid 451 through 463 No H-bonds generated for 'chain 'A' and resid 451 through 463' Processing helix chain 'A' and resid 479 through 491 No H-bonds generated for 'chain 'A' and resid 479 through 491' Processing helix chain 'A' and resid 500 through 512 No H-bonds generated for 'chain 'A' and resid 500 through 512' Processing helix chain 'A' and resid 514 through 528 No H-bonds generated for 'chain 'A' and resid 514 through 528' Processing helix chain 'A' and resid 531 through 549 No H-bonds generated for 'chain 'A' and resid 531 through 549' Processing helix chain 'A' and resid 579 through 592 No H-bonds generated for 'chain 'A' and resid 579 through 592' Processing helix chain 'A' and resid 600 through 612 No H-bonds generated for 'chain 'A' and resid 600 through 612' Processing helix chain 'A' and resid 615 through 630 No H-bonds generated for 'chain 'A' and resid 615 through 630' Processing helix chain 'A' and resid 645 through 666 No H-bonds generated for 'chain 'A' and resid 645 through 666' Processing helix chain 'A' and resid 668 through 679 No H-bonds generated for 'chain 'A' and resid 668 through 679' Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 683 through 688 No H-bonds generated for 'chain 'A' and resid 683 through 688' Processing helix chain 'A' and resid 689 through 700 No H-bonds generated for 'chain 'A' and resid 689 through 700' Processing helix chain 'A' and resid 704 through 718 No H-bonds generated for 'chain 'A' and resid 704 through 718' Processing helix chain 'A' and resid 722 through 744 No H-bonds generated for 'chain 'A' and resid 722 through 744' Processing helix chain 'A' and resid 746 through 764 No H-bonds generated for 'chain 'A' and resid 746 through 764' Processing helix chain 'A' and resid 764 through 769 No H-bonds generated for 'chain 'A' and resid 764 through 769' Processing helix chain 'A' and resid 771 through 784 No H-bonds generated for 'chain 'A' and resid 771 through 784' Processing helix chain 'A' and resid 792 through 810 No H-bonds generated for 'chain 'A' and resid 792 through 810' Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 816 through 829 No H-bonds generated for 'chain 'A' and resid 816 through 829' Processing helix chain 'A' and resid 836 through 852 No H-bonds generated for 'chain 'A' and resid 836 through 852' Processing helix chain 'A' and resid 855 through 861 No H-bonds generated for 'chain 'A' and resid 855 through 861' Processing helix chain 'A' and resid 863 through 875 No H-bonds generated for 'chain 'A' and resid 863 through 875' Processing helix chain 'A' and resid 877 through 891 No H-bonds generated for 'chain 'A' and resid 877 through 891' Processing helix chain 'A' and resid 895 through 903 No H-bonds generated for 'chain 'A' and resid 895 through 903' Processing helix chain 'A' and resid 934 through 941 No H-bonds generated for 'chain 'A' and resid 934 through 941' Processing helix chain 'A' and resid 942 through 960 No H-bonds generated for 'chain 'A' and resid 942 through 960' Processing helix chain 'A' and resid 963 through 983 No H-bonds generated for 'chain 'A' and resid 963 through 983' Processing helix chain 'A' and resid 984 through 988 No H-bonds generated for 'chain 'A' and resid 984 through 988' Processing helix chain 'A' and resid 989 through 1004 No H-bonds generated for 'chain 'A' and resid 989 through 1004' Processing helix chain 'A' and resid 1006 through 1024 No H-bonds generated for 'chain 'A' and resid 1006 through 1024' Processing helix chain 'A' and resid 1027 through 1042 No H-bonds generated for 'chain 'A' and resid 1027 through 1042' Processing helix chain 'A' and resid 1045 through 1064 No H-bonds generated for 'chain 'A' and resid 1045 through 1064' Processing helix chain 'A' and resid 1065 through 1069 No H-bonds generated for 'chain 'A' and resid 1065 through 1069' Processing helix chain 'A' and resid 1070 through 1084 No H-bonds generated for 'chain 'A' and resid 1070 through 1084' Processing helix chain 'A' and resid 1087 through 1089 No H-bonds generated for 'chain 'A' and resid 1087 through 1089' Processing helix chain 'A' and resid 1090 through 1104 No H-bonds generated for 'chain 'A' and resid 1090 through 1104' Processing helix chain 'A' and resid 1105 through 1109 No H-bonds generated for 'chain 'A' and resid 1105 through 1109' Processing helix chain 'A' and resid 1110 through 1124 No H-bonds generated for 'chain 'A' and resid 1110 through 1124' Processing helix chain 'A' and resid 1128 through 1146 No H-bonds generated for 'chain 'A' and resid 1128 through 1146' Processing helix chain 'A' and resid 1151 through 1166 No H-bonds generated for 'chain 'A' and resid 1151 through 1166' Processing helix chain 'A' and resid 1169 through 1185 No H-bonds generated for 'chain 'A' and resid 1169 through 1185' Processing helix chain 'A' and resid 1186 through 1190 No H-bonds generated for 'chain 'A' and resid 1186 through 1190' Processing helix chain 'A' and resid 1191 through 1202 No H-bonds generated for 'chain 'A' and resid 1191 through 1202' Processing helix chain 'A' and resid 1206 through 1219 No H-bonds generated for 'chain 'A' and resid 1206 through 1219' Processing helix chain 'A' and resid 1263 through 1270 No H-bonds generated for 'chain 'A' and resid 1263 through 1270' Processing helix chain 'A' and resid 1276 through 1295 No H-bonds generated for 'chain 'A' and resid 1276 through 1295' Processing helix chain 'A' and resid 1297 through 1302 No H-bonds generated for 'chain 'A' and resid 1297 through 1302' Processing helix chain 'A' and resid 1303 through 1310 No H-bonds generated for 'chain 'A' and resid 1303 through 1310' Processing helix chain 'A' and resid 1310 through 1317 No H-bonds generated for 'chain 'A' and resid 1310 through 1317' Processing helix chain 'A' and resid 1317 through 1329 No H-bonds generated for 'chain 'A' and resid 1317 through 1329' Processing helix chain 'A' and resid 1331 through 1347 No H-bonds generated for 'chain 'A' and resid 1331 through 1347' Processing helix chain 'A' and resid 1350 through 1367 No H-bonds generated for 'chain 'A' and resid 1350 through 1367' Processing helix chain 'A' and resid 1376 through 1380 No H-bonds generated for 'chain 'A' and resid 1376 through 1380' Processing helix chain 'A' and resid 1381 through 1390 No H-bonds generated for 'chain 'A' and resid 1381 through 1390' Processing helix chain 'A' and resid 1392 through 1407 No H-bonds generated for 'chain 'A' and resid 1392 through 1407' Processing helix chain 'A' and resid 1409 through 1423 No H-bonds generated for 'chain 'A' and resid 1409 through 1423' Processing helix chain 'A' and resid 1425 through 1441 No H-bonds generated for 'chain 'A' and resid 1425 through 1441' Processing helix chain 'A' and resid 1446 through 1453 No H-bonds generated for 'chain 'A' and resid 1446 through 1453' Processing helix chain 'A' and resid 1455 through 1470 No H-bonds generated for 'chain 'A' and resid 1455 through 1470' Processing helix chain 'A' and resid 1473 through 1488 No H-bonds generated for 'chain 'A' and resid 1473 through 1488' Processing helix chain 'A' and resid 1489 through 1500 No H-bonds generated for 'chain 'A' and resid 1489 through 1500' Processing helix chain 'A' and resid 1505 through 1524 No H-bonds generated for 'chain 'A' and resid 1505 through 1524' Processing helix chain 'A' and resid 1525 through 1536 No H-bonds generated for 'chain 'A' and resid 1525 through 1536' Processing helix chain 'A' and resid 1540 through 1554 No H-bonds generated for 'chain 'A' and resid 1540 through 1554' Processing helix chain 'A' and resid 1556 through 1581 No H-bonds generated for 'chain 'A' and resid 1556 through 1581' Processing helix chain 'A' and resid 1582 through 1608 No H-bonds generated for 'chain 'A' and resid 1582 through 1608' Processing helix chain 'A' and resid 1611 through 1626 No H-bonds generated for 'chain 'A' and resid 1611 through 1626' Processing helix chain 'A' and resid 1629 through 1641 No H-bonds generated for 'chain 'A' and resid 1629 through 1641' Processing helix chain 'A' and resid 1645 through 1648 No H-bonds generated for 'chain 'A' and resid 1645 through 1648' Processing helix chain 'A' and resid 1649 through 1663 No H-bonds generated for 'chain 'A' and resid 1649 through 1663' Processing helix chain 'A' and resid 1665 through 1678 No H-bonds generated for 'chain 'A' and resid 1665 through 1678' Processing helix chain 'A' and resid 1693 through 1707 No H-bonds generated for 'chain 'A' and resid 1693 through 1707' Processing helix chain 'A' and resid 1709 through 1732 No H-bonds generated for 'chain 'A' and resid 1709 through 1732' Processing helix chain 'A' and resid 1737 through 1762 No H-bonds generated for 'chain 'A' and resid 1737 through 1762' Processing helix chain 'A' and resid 1767 through 1783 No H-bonds generated for 'chain 'A' and resid 1767 through 1783' Processing helix chain 'A' and resid 1786 through 1812 No H-bonds generated for 'chain 'A' and resid 1786 through 1812' Processing helix chain 'A' and resid 1868 through 1896 No H-bonds generated for 'chain 'A' and resid 1868 through 1896' Processing helix chain 'A' and resid 1899 through 1914 No H-bonds generated for 'chain 'A' and resid 1899 through 1914' Processing helix chain 'A' and resid 1916 through 1930 No H-bonds generated for 'chain 'A' and resid 1916 through 1930' Processing helix chain 'A' and resid 1933 through 1937 No H-bonds generated for 'chain 'A' and resid 1933 through 1937' Processing helix chain 'A' and resid 1938 through 1945 No H-bonds generated for 'chain 'A' and resid 1938 through 1945' Processing helix chain 'A' and resid 1950 through 1967 No H-bonds generated for 'chain 'A' and resid 1950 through 1967' Processing helix chain 'A' and resid 1968 through 1971 No H-bonds generated for 'chain 'A' and resid 1968 through 1971' Processing helix chain 'A' and resid 1972 through 1981 No H-bonds generated for 'chain 'A' and resid 1972 through 1981' Processing helix chain 'A' and resid 1984 through 2002 No H-bonds generated for 'chain 'A' and resid 1984 through 2002' Processing helix chain 'A' and resid 2003 through 2021 No H-bonds generated for 'chain 'A' and resid 2003 through 2021' Processing helix chain 'A' and resid 2022 through 2039 No H-bonds generated for 'chain 'A' and resid 2022 through 2039' Processing helix chain 'A' and resid 2043 through 2059 No H-bonds generated for 'chain 'A' and resid 2043 through 2059' Processing helix chain 'A' and resid 2064 through 2074 No H-bonds generated for 'chain 'A' and resid 2064 through 2074' Processing helix chain 'A' and resid 2074 through 2091 No H-bonds generated for 'chain 'A' and resid 2074 through 2091' Processing helix chain 'A' and resid 2093 through 2115 No H-bonds generated for 'chain 'A' and resid 2093 through 2115' Processing helix chain 'A' and resid 2116 through 2118 No H-bonds generated for 'chain 'A' and resid 2116 through 2118' Processing helix chain 'A' and resid 2123 through 2127 No H-bonds generated for 'chain 'A' and resid 2123 through 2127' Processing helix chain 'A' and resid 2127 through 2133 No H-bonds generated for 'chain 'A' and resid 2127 through 2133' Processing helix chain 'A' and resid 2192 through 2212 No H-bonds generated for 'chain 'A' and resid 2192 through 2212' Processing helix chain 'A' and resid 2212 through 2219 No H-bonds generated for 'chain 'A' and resid 2212 through 2219' Processing helix chain 'A' and resid 2246 through 2257 No H-bonds generated for 'chain 'A' and resid 2246 through 2257' Processing helix chain 'A' and resid 2262 through 2272 No H-bonds generated for 'chain 'A' and resid 2262 through 2272' Processing helix chain 'A' and resid 2274 through 2278 No H-bonds generated for 'chain 'A' and resid 2274 through 2278' Processing helix chain 'A' and resid 2279 through 2293 No H-bonds generated for 'chain 'A' and resid 2279 through 2293' Processing helix chain 'A' and resid 2297 through 2307 No H-bonds generated for 'chain 'A' and resid 2297 through 2307' Processing helix chain 'A' and resid 2309 through 2335 No H-bonds generated for 'chain 'A' and resid 2309 through 2335' Processing helix chain 'A' and resid 2363 through 2368 No H-bonds generated for 'chain 'A' and resid 2363 through 2368' Processing helix chain 'A' and resid 2380 through 2387 No H-bonds generated for 'chain 'A' and resid 2380 through 2387' Processing helix chain 'A' and resid 2394 through 2410 No H-bonds generated for 'chain 'A' and resid 2394 through 2410' Processing helix chain 'A' and resid 2410 through 2424 No H-bonds generated for 'chain 'A' and resid 2410 through 2424' Processing helix chain 'A' and resid 2427 through 2435 No H-bonds generated for 'chain 'A' and resid 2427 through 2435' Processing helix chain 'A' and resid 2493 through 2510 No H-bonds generated for 'chain 'A' and resid 2493 through 2510' Processing helix chain 'A' and resid 2520 through 2534 No H-bonds generated for 'chain 'A' and resid 2520 through 2534' Processing helix chain 'A' and resid 2534 through 2541 No H-bonds generated for 'chain 'A' and resid 2534 through 2541' Processing helix chain 'A' and resid 2542 through 2546 No H-bonds generated for 'chain 'A' and resid 2542 through 2546' Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 89 through 94 removed outlier: 4.047A pdb=" N MET E 93 " --> pdb=" O ASP E 89 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY E 94 " --> pdb=" O PRO E 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 94' Processing helix chain 'E' and resid 94 through 114 removed outlier: 4.029A pdb=" N TRP E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 141 Processing helix chain 'E' and resid 179 through 186 removed outlier: 3.593A pdb=" N MET E 186 " --> pdb=" O LEU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 219 removed outlier: 4.135A pdb=" N ILE E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL E 219 " --> pdb=" O GLN E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 269 Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 285 removed outlier: 6.331A pdb=" N CYS E 283 " --> pdb=" O MET E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 307 through 328 Processing helix chain 'E' and resid 329 through 338 removed outlier: 3.688A pdb=" N ARG E 338 " --> pdb=" O GLN E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 359 removed outlier: 3.857A pdb=" N LEU E 352 " --> pdb=" O ARG E 348 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 359 " --> pdb=" O ARG E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 390 removed outlier: 4.223A pdb=" N GLN E 380 " --> pdb=" O HIS E 376 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 398 Processing helix chain 'E' and resid 407 through 422 removed outlier: 4.030A pdb=" N MET E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 440 Processing helix chain 'E' and resid 445 through 459 removed outlier: 3.622A pdb=" N LEU E 459 " --> pdb=" O ARG E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 471 removed outlier: 3.506A pdb=" N GLY E 471 " --> pdb=" O ALA E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 479 Processing helix chain 'E' and resid 480 through 482 No H-bonds generated for 'chain 'E' and resid 480 through 482' Processing helix chain 'E' and resid 486 through 502 removed outlier: 4.522A pdb=" N LEU E 490 " --> pdb=" O GLU E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 512 Processing helix chain 'E' and resid 514 through 523 removed outlier: 3.515A pdb=" N PHE E 518 " --> pdb=" O GLY E 514 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL E 521 " --> pdb=" O TYR E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 543 Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 557 through 565 Processing helix chain 'E' and resid 570 through 585 removed outlier: 3.826A pdb=" N TRP E 585 " --> pdb=" O LEU E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 Processing helix chain 'E' and resid 599 through 605 Processing helix chain 'E' and resid 606 through 610 Processing helix chain 'E' and resid 612 through 629 removed outlier: 4.001A pdb=" N ASN E 629 " --> pdb=" O THR E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 649 removed outlier: 3.911A pdb=" N THR E 638 " --> pdb=" O THR E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 674 removed outlier: 3.563A pdb=" N LEU E 670 " --> pdb=" O ALA E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 685 removed outlier: 3.720A pdb=" N THR E 680 " --> pdb=" O SER E 676 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 820 Processing helix chain 'E' and resid 823 through 839 removed outlier: 3.548A pdb=" N ILE E 837 " --> pdb=" O VAL E 833 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA E 838 " --> pdb=" O LEU E 834 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR E 839 " --> pdb=" O ASN E 835 " (cutoff:3.500A) Processing helix chain 'E' and resid 950 through 954 removed outlier: 3.627A pdb=" N ALA E 953 " --> pdb=" O PHE E 950 " (cutoff:3.500A) Processing helix chain 'E' and resid 958 through 969 removed outlier: 4.008A pdb=" N TYR E 966 " --> pdb=" O TRP E 962 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE E 967 " --> pdb=" O SER E 963 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA E 968 " --> pdb=" O ALA E 964 " (cutoff:3.500A) Processing helix chain 'E' and resid 982 through 1008 Processing helix chain 'I' and resid 359 through 364 Processing helix chain 'I' and resid 384 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 2120 through 2122 WARNING: can't find one or more strands! previous: chain 'A' and resid 2120 through 2122 current: chain 'A' and resid 2159 through 2161 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 2153 through 2156 WARNING: can't find one or more strands! previous: chain 'A' and resid 2153 through 2156 current: chain 'A' and resid 2173 through 2176 WARNING: can't find one or more strands! previous: chain 'A' and resid 2173 through 2176 current: chain 'A' and resid 2181 through 2187 WARNING: can't find one or more strands! previous: chain 'A' and resid 2181 through 2187 current: chain 'A' and resid 2235 through 2238 WARNING: can't find one or more strands! previous: chain 'A' and resid 2235 through 2238 current: chain 'A' and resid 2227 through 2229 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 2243 through 2245 WARNING: can't find one or more strands! previous: chain 'A' and resid 2243 through 2245 current: chain 'A' and resid 2344 through 2347 WARNING: can't find one or more strands! previous: chain 'A' and resid 2344 through 2347 current: chain 'A' and resid 2353 through 2355 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 24 through 27 removed outlier: 4.195A pdb=" N LEU C 15 " --> pdb=" O TRP C 27 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA C 18 " --> pdb=" O CYS C 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.733A pdb=" N ILE C 79 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 88 through 91 removed outlier: 6.501A pdb=" N GLY C 103 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 91 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR C 101 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 102 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 110 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY C 104 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 134 through 136 Processing sheet with id=AA8, first strand: chain 'C' and resid 173 through 178 removed outlier: 3.641A pdb=" N SER C 175 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N CYS C 194 " --> pdb=" O LYS C 215 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS C 215 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL C 196 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 223 through 228 removed outlier: 3.623A pdb=" N GLN C 225 " --> pdb=" O CYS C 238 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER C 239 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR C 256 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG C 248 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 254 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 277 through 278 removed outlier: 6.783A pdb=" N ALA C 294 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU C 307 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU C 296 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 118 through 123 removed outlier: 3.542A pdb=" N LEU E 62 " --> pdb=" O LYS E 120 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER E 59 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N HIS E 149 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA E 61 " --> pdb=" O HIS E 149 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASN E 151 " --> pdb=" O ALA E 61 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL E 63 " --> pdb=" O ASN E 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 163 through 167 Processing sheet with id=AB4, first strand: chain 'E' and resid 1015 through 1016 removed outlier: 3.989A pdb=" N ASP E1015 " --> pdb=" O SER E1329 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER E1329 " --> pdb=" O ASP E1015 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN E1020 " --> pdb=" O ILE E1325 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 1015 through 1016 removed outlier: 3.989A pdb=" N ASP E1015 " --> pdb=" O SER E1329 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER E1329 " --> pdb=" O ASP E1015 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER E1326 " --> pdb=" O VAL E1318 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL E1318 " --> pdb=" O SER E1326 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E1316 " --> pdb=" O TYR E1328 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 1028 through 1031 removed outlier: 4.318A pdb=" N VAL E1028 " --> pdb=" O ALA E1041 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS E1030 " --> pdb=" O ALA E1039 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E1039 " --> pdb=" O LYS E1030 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE E1048 " --> pdb=" O ASP E1058 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP E1058 " --> pdb=" O PHE E1048 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 1070 through 1073 removed outlier: 3.848A pdb=" N ALA E1072 " --> pdb=" O ALA E1087 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E1087 " --> pdb=" O ALA E1072 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA E1092 " --> pdb=" O THR E1088 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE E1093 " --> pdb=" O ALA E1111 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA E1111 " --> pdb=" O ILE E1093 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL E1095 " --> pdb=" O VAL E1109 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 1127 through 1128 Processing sheet with id=AB9, first strand: chain 'E' and resid 1131 through 1132 removed outlier: 3.660A pdb=" N GLU E1132 " --> pdb=" O LEU E1137 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU E1137 " --> pdb=" O GLU E1132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 1146 through 1151 removed outlier: 4.164A pdb=" N GLN E1159 " --> pdb=" O ILE E1149 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP E1151 " --> pdb=" O LYS E1157 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS E1157 " --> pdb=" O ASP E1151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 1169 through 1173 removed outlier: 3.665A pdb=" N SER E1171 " --> pdb=" O GLY E1184 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE E1190 " --> pdb=" O THR E1206 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR E1206 " --> pdb=" O ILE E1190 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL E1192 " --> pdb=" O VAL E1204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 1227 through 1230 removed outlier: 3.919A pdb=" N SER E1229 " --> pdb=" O ARG E1237 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN E1248 " --> pdb=" O ILE E1238 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 1268 through 1269 removed outlier: 3.868A pdb=" N ASN E1288 " --> pdb=" O ILE E1279 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 329 through 333 removed outlier: 5.014A pdb=" N SER I 374 " --> pdb=" O GLU I 402 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 342 through 344 removed outlier: 6.540A pdb=" N VAL I 343 " --> pdb=" O GLN I 353 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1671 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: 11.21 Time building geometry restraints manager: 12.26 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: 9584 1.34 - 1.46: 6072 1.46 - 1.58: 13789 1.58 - 1.69: 6 1.69 - 1.81: 310 Bond restraints: 29761 Sorted by residual: bond pdb=" O12 IHP A2601 " pdb=" P2 IHP A2601 " ideal model delta sigma weight residual 1.675 1.598 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 1.671 1.602 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C5 IHP A2601 " pdb=" O15 IHP A2601 " ideal model delta sigma weight residual 1.389 1.444 -0.055 2.00e-02 2.50e+03 7.44e+00 bond pdb=" O15 IHP A2601 " pdb=" P5 IHP A2601 " ideal model delta sigma weight residual 1.675 1.623 0.052 2.00e-02 2.50e+03 6.77e+00 bond pdb=" C1 IHP A2601 " pdb=" O11 IHP A2601 " ideal model delta sigma weight residual 1.392 1.443 -0.051 2.00e-02 2.50e+03 6.62e+00 ... (remaining 29756 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.93: 944 106.93 - 113.71: 16695 113.71 - 120.49: 11099 120.49 - 127.27: 11253 127.27 - 134.05: 399 Bond angle restraints: 40390 Sorted by residual: angle pdb=" C LEU A 757 " pdb=" N GLY A 758 " pdb=" CA GLY A 758 " ideal model delta sigma weight residual 119.99 123.82 -3.83 1.13e+00 7.83e-01 1.15e+01 angle pdb=" C GLY I 323 " pdb=" N ALA I 324 " pdb=" CA ALA I 324 " ideal model delta sigma weight residual 121.80 128.61 -6.81 2.44e+00 1.68e-01 7.79e+00 angle pdb=" CA LYS A1024 " pdb=" CB LYS A1024 " pdb=" CG LYS A1024 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.61e+00 angle pdb=" C PRO E 80 " pdb=" N CYS E 81 " pdb=" CA CYS E 81 " ideal model delta sigma weight residual 121.76 127.64 -5.88 2.19e+00 2.09e-01 7.20e+00 angle pdb=" CA PHE A 610 " pdb=" CB PHE A 610 " pdb=" CG PHE A 610 " ideal model delta sigma weight residual 113.80 116.47 -2.67 1.00e+00 1.00e+00 7.10e+00 ... (remaining 40385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 16257 17.27 - 34.54: 1355 34.54 - 51.82: 288 51.82 - 69.09: 74 69.09 - 86.36: 18 Dihedral angle restraints: 17992 sinusoidal: 7263 harmonic: 10729 Sorted by residual: dihedral pdb=" CA UNK A 17 " pdb=" C UNK A 17 " pdb=" N UNK A 18 " pdb=" CA UNK A 18 " ideal model delta harmonic sigma weight residual 180.00 151.36 28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA PHE E1060 " pdb=" C PHE E1060 " pdb=" N HIS E1061 " pdb=" CA HIS E1061 " ideal model delta harmonic sigma weight residual 180.00 153.46 26.54 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA ALA I 324 " pdb=" C ALA I 324 " pdb=" N PRO I 325 " pdb=" CA PRO I 325 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 17989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3999 0.058 - 0.117: 532 0.117 - 0.175: 59 0.175 - 0.233: 1 0.233 - 0.292: 3 Chirality restraints: 4594 Sorted by residual: chirality pdb=" C1 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C6 IHP A2601 " pdb=" O11 IHP A2601 " both_signs ideal model delta sigma weight residual False 2.32 2.61 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CG LEU A 395 " pdb=" CB LEU A 395 " pdb=" CD1 LEU A 395 " pdb=" CD2 LEU A 395 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C3 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C4 IHP A2601 " pdb=" O13 IHP A2601 " both_signs ideal model delta sigma weight residual False -2.34 -2.60 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 4591 not shown) Planarity restraints: 5143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A1157 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO A1158 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 324 " -0.038 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO I 325 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO I 325 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 325 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E1105 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO E1106 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO E1106 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E1106 " -0.031 5.00e-02 4.00e+02 ... (remaining 5140 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5223 2.78 - 3.31: 29601 3.31 - 3.84: 48405 3.84 - 4.37: 57844 4.37 - 4.90: 95066 Nonbonded interactions: 236139 Sorted by model distance: nonbonded pdb=" O GLY A2337 " pdb=" NH1 ARG A2339 " model vdw 2.245 2.520 nonbonded pdb=" O ALA A1268 " pdb=" NE1 TRP A1283 " model vdw 2.251 2.520 nonbonded pdb=" O THR E1163 " pdb=" OH TYR E1193 " model vdw 2.255 2.440 nonbonded pdb=" O THR A 484 " pdb=" OG SER A 487 " model vdw 2.259 2.440 nonbonded pdb=" O LEU I 319 " pdb=" OH TYR I 326 " model vdw 2.281 2.440 ... (remaining 236134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.920 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: 1.160 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 77.190 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.130 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 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 : 0.002 0.077 29761 Z= 0.159 Angle : 0.521 7.784 40390 Z= 0.280 Chirality : 0.040 0.292 4594 Planarity : 0.005 0.057 5143 Dihedral : 13.932 86.360 11000 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.09 % Favored : 94.86 % Rotamer: Outliers : 2.69 % Allowed : 6.14 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.12), residues: 3559 helix: -1.44 (0.10), residues: 2088 sheet: -3.26 (0.23), residues: 348 loop : -1.44 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2023 HIS 0.007 0.001 HIS E1315 PHE 0.025 0.001 PHE A 610 TYR 0.012 0.001 TYR E 475 ARG 0.006 0.000 ARG A1161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 674 time to evaluate : 4.357 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: 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 532 LYS cc_start: 0.2684 (OUTLIER) cc_final: 0.2381 (tptt) REVERT: A 780 ILE cc_start: 0.9036 (mt) cc_final: 0.8693 (pt) REVERT: A 805 LEU cc_start: 0.9192 (mt) cc_final: 0.8861 (mt) REVERT: A 808 VAL cc_start: 0.7858 (t) cc_final: 0.7538 (t) REVERT: A 1074 LEU cc_start: 0.9120 (mt) cc_final: 0.8499 (mp) REVERT: A 1362 GLU cc_start: 0.7978 (tt0) cc_final: 0.7754 (tp30) REVERT: A 1401 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7377 (mt-10) REVERT: A 1455 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7928 (tp30) REVERT: A 1546 TYR cc_start: 0.8341 (m-80) cc_final: 0.7986 (m-80) REVERT: A 1673 LEU cc_start: 0.9278 (mt) cc_final: 0.9017 (mt) REVERT: A 1752 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8744 (tt) REVERT: A 1809 GLN cc_start: 0.8283 (mt0) cc_final: 0.7966 (tm-30) REVERT: A 1913 TYR cc_start: 0.7417 (m-80) cc_final: 0.7156 (m-80) REVERT: A 2021 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9052 (pt) REVERT: A 2051 LEU cc_start: 0.8674 (mt) cc_final: 0.8437 (pp) REVERT: A 2161 GLN cc_start: 0.8083 (tm130) cc_final: 0.7827 (tm-30) REVERT: A 2199 MET cc_start: 0.8769 (mmt) cc_final: 0.8410 (mmt) REVERT: C 155 TRP cc_start: 0.7411 (t60) cc_final: 0.7122 (t60) REVERT: C 197 TRP cc_start: 0.7049 (m100) cc_final: 0.6094 (m100) REVERT: C 315 VAL cc_start: 0.7012 (t) cc_final: 0.6658 (t) REVERT: E 89 ASP cc_start: 0.8756 (t0) cc_final: 0.8287 (t0) REVERT: E 585 TRP cc_start: 0.4133 (p90) cc_final: 0.3872 (p90) REVERT: E 831 MET cc_start: 0.6292 (tpp) cc_final: 0.5524 (tpt) REVERT: E 1131 TRP cc_start: 0.8028 (t-100) cc_final: 0.7374 (t-100) REVERT: E 1132 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7162 (mm-30) REVERT: E 1172 LEU cc_start: 0.8611 (tt) cc_final: 0.8181 (tp) REVERT: E 1181 ILE cc_start: 0.8423 (mp) cc_final: 0.8222 (mm) REVERT: E 1224 ASP cc_start: 0.7763 (m-30) cc_final: 0.7011 (p0) REVERT: E 1236 VAL cc_start: 0.6529 (t) cc_final: 0.6285 (t) REVERT: E 1309 PHE cc_start: 0.6166 (m-80) cc_final: 0.5484 (m-10) REVERT: I 373 VAL cc_start: 0.7865 (m) cc_final: 0.7202 (t) REVERT: I 405 GLU cc_start: 0.6879 (tt0) cc_final: 0.6482 (tt0) outliers start: 85 outliers final: 11 residues processed: 735 average time/residue: 0.4810 time to fit residues: 546.8939 Evaluate side-chains 347 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 333 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 959 PHE Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1299 SER Chi-restraints excluded: chain A residue 1652 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 1323 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 0.6980 chunk 275 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 212 optimal weight: 0.8980 chunk 330 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 HIS C 242 GLN E 636 HIS E1210 HIS ** E1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 376 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29761 Z= 0.240 Angle : 0.633 11.727 40390 Z= 0.315 Chirality : 0.042 0.414 4594 Planarity : 0.005 0.071 5143 Dihedral : 5.030 52.460 4023 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.33 % Favored : 97.64 % Rotamer: Outliers : 2.62 % Allowed : 12.43 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3559 helix: 0.54 (0.11), residues: 2092 sheet: -2.90 (0.23), residues: 357 loop : -0.90 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 27 HIS 0.009 0.001 HIS E1312 PHE 0.035 0.002 PHE A2421 TYR 0.019 0.001 TYR I 385 ARG 0.015 0.001 ARG C 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 340 time to evaluate : 3.486 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: 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: symmetry clash revert: symmetry clash REVERT: A 488 MET cc_start: -0.0073 (mmp) cc_final: -0.0400 (tpp) REVERT: A 532 LYS cc_start: 0.3395 (OUTLIER) cc_final: 0.3031 (tptt) REVERT: A 548 MET cc_start: 0.4368 (mtt) cc_final: 0.4054 (mmm) REVERT: A 686 HIS cc_start: 0.8231 (m90) cc_final: 0.6813 (t-90) REVERT: A 772 MET cc_start: 0.8114 (tpt) cc_final: 0.7520 (tmm) REVERT: A 1174 MET cc_start: 0.8311 (tpp) cc_final: 0.8032 (mmm) REVERT: A 1477 MET cc_start: 0.8466 (tpp) cc_final: 0.8206 (tpp) REVERT: A 1566 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8334 (ttmt) REVERT: A 1575 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8955 (tt) REVERT: A 1673 LEU cc_start: 0.9273 (mt) cc_final: 0.9005 (mt) REVERT: A 1809 GLN cc_start: 0.8391 (mt0) cc_final: 0.8064 (tm-30) REVERT: A 2051 LEU cc_start: 0.8749 (mt) cc_final: 0.8479 (pp) REVERT: A 2161 GLN cc_start: 0.8152 (tm130) cc_final: 0.7875 (tm-30) REVERT: A 2199 MET cc_start: 0.8789 (mmt) cc_final: 0.8453 (mmt) REVERT: A 2298 ASP cc_start: 0.8093 (m-30) cc_final: 0.7515 (m-30) REVERT: C 100 MET cc_start: 0.8640 (tmm) cc_final: 0.8313 (tmm) REVERT: C 273 MET cc_start: 0.7874 (ttm) cc_final: 0.7638 (ttm) REVERT: E 28 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7810 (mm) REVERT: E 31 MET cc_start: 0.8262 (ppp) cc_final: 0.7368 (mmt) REVERT: E 89 ASP cc_start: 0.8729 (t0) cc_final: 0.8391 (t0) REVERT: E 342 LEU cc_start: 0.7900 (tp) cc_final: 0.7612 (tp) REVERT: E 378 MET cc_start: 0.8893 (mmm) cc_final: 0.8434 (mmm) REVERT: E 431 GLU cc_start: 0.7283 (pt0) cc_final: 0.7043 (tt0) REVERT: E 1010 ILE cc_start: 0.6705 (mm) cc_final: 0.6328 (tp) REVERT: E 1012 ARG cc_start: 0.5140 (mmp80) cc_final: 0.4485 (mmp80) REVERT: E 1037 CYS cc_start: 0.5364 (m) cc_final: 0.4930 (m) REVERT: E 1073 MET cc_start: 0.6958 (mtp) cc_final: 0.6677 (mtm) REVERT: E 1131 TRP cc_start: 0.7592 (t-100) cc_final: 0.7346 (t-100) REVERT: E 1132 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7389 (pt0) REVERT: E 1156 MET cc_start: 0.6995 (mmm) cc_final: 0.6776 (mmt) REVERT: E 1172 LEU cc_start: 0.8522 (tt) cc_final: 0.8233 (tt) REVERT: E 1224 ASP cc_start: 0.7853 (m-30) cc_final: 0.7166 (p0) REVERT: E 1309 PHE cc_start: 0.6174 (m-80) cc_final: 0.5699 (m-10) outliers start: 83 outliers final: 49 residues processed: 399 average time/residue: 0.4170 time to fit residues: 266.6450 Evaluate side-chains 327 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 275 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 940 ASN Chi-restraints excluded: chain A residue 959 PHE Chi-restraints excluded: chain A residue 968 HIS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1502 THR Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2217 ARG Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 670 LEU Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 1058 ASP Chi-restraints excluded: chain E residue 1105 ASN Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1197 MET Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain E residue 1325 ILE Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 331 optimal weight: 8.9990 chunk 357 optimal weight: 4.9990 chunk 294 optimal weight: 0.8980 chunk 328 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 265 optimal weight: 0.1980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 311 HIS E 281 GLN E 969 GLN ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 29761 Z= 0.294 Angle : 0.657 10.834 40390 Z= 0.323 Chirality : 0.043 0.263 4594 Planarity : 0.005 0.065 5143 Dihedral : 5.056 56.950 4014 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.38 % Rotamer: Outliers : 3.32 % Allowed : 12.24 % Favored : 84.44 % 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: -0.17 (0.14), residues: 3559 helix: 0.87 (0.11), residues: 2063 sheet: -2.73 (0.24), residues: 339 loop : -0.92 (0.18), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1916 HIS 0.010 0.001 HIS A2410 PHE 0.029 0.002 PHE A2421 TYR 0.023 0.002 TYR A2105 ARG 0.021 0.001 ARG A2086 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 302 time to evaluate : 3.499 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.0927 (mtt) cc_final: 0.0658 (mpp) REVERT: A 439 LEU cc_start: -0.2991 (OUTLIER) cc_final: -0.3264 (tp) REVERT: A 532 LYS cc_start: 0.4034 (OUTLIER) cc_final: 0.3420 (tptp) REVERT: A 548 MET cc_start: 0.4281 (mtt) cc_final: 0.3787 (mmt) REVERT: A 718 LEU cc_start: 0.5350 (OUTLIER) cc_final: 0.5081 (tp) REVERT: A 752 GLN cc_start: 0.8493 (mt0) cc_final: 0.8129 (mt0) REVERT: A 1477 MET cc_start: 0.8579 (tpp) cc_final: 0.8352 (tpp) REVERT: A 1552 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8633 (mm) REVERT: A 1809 GLN cc_start: 0.8555 (mt0) cc_final: 0.8236 (tm-30) REVERT: A 2031 LEU cc_start: 0.8654 (mp) cc_final: 0.8291 (tp) REVERT: A 2051 LEU cc_start: 0.8546 (mt) cc_final: 0.8284 (pp) REVERT: A 2076 ARG cc_start: 0.8448 (ttp-110) cc_final: 0.8248 (ttp-110) REVERT: A 2118 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8208 (pp) REVERT: A 2161 GLN cc_start: 0.8199 (tm130) cc_final: 0.7836 (tm-30) REVERT: A 2187 LYS cc_start: 0.8686 (mmtp) cc_final: 0.8451 (mmmt) REVERT: A 2199 MET cc_start: 0.8785 (mmt) cc_final: 0.8436 (mmt) REVERT: A 2298 ASP cc_start: 0.8250 (m-30) cc_final: 0.7732 (m-30) REVERT: C 99 TRP cc_start: 0.5308 (m100) cc_final: 0.4725 (m100) REVERT: C 100 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8355 (tmm) REVERT: E 33 LYS cc_start: 0.7940 (mmtt) cc_final: 0.7721 (mtpt) REVERT: E 89 ASP cc_start: 0.8799 (t0) cc_final: 0.8287 (t0) REVERT: E 294 LEU cc_start: 0.8993 (mt) cc_final: 0.8736 (mt) REVERT: E 342 LEU cc_start: 0.7907 (tp) cc_final: 0.7699 (tp) REVERT: E 378 MET cc_start: 0.8958 (mmm) cc_final: 0.8503 (mmm) REVERT: E 431 GLU cc_start: 0.7371 (pt0) cc_final: 0.7143 (tt0) REVERT: E 961 ASP cc_start: 0.8046 (t70) cc_final: 0.7724 (t70) REVERT: E 1088 THR cc_start: 0.4265 (OUTLIER) cc_final: 0.4041 (p) REVERT: E 1127 MET cc_start: 0.6678 (tpt) cc_final: 0.6359 (tpp) REVERT: E 1218 SER cc_start: 0.7163 (t) cc_final: 0.6932 (m) REVERT: E 1309 PHE cc_start: 0.6188 (m-80) cc_final: 0.5678 (m-10) outliers start: 105 outliers final: 56 residues processed: 376 average time/residue: 0.3990 time to fit residues: 244.8426 Evaluate side-chains 326 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 263 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 940 ASN Chi-restraints excluded: chain A residue 959 PHE Chi-restraints excluded: chain A residue 968 HIS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1504 VAL Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1952 LEU Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2427 LEU Chi-restraints excluded: chain A residue 2501 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 1058 ASP Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1105 ASN Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 10.0000 chunk 248 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 332 optimal weight: 0.7980 chunk 351 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 314 optimal weight: 0.0670 chunk 94 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29761 Z= 0.175 Angle : 0.557 10.185 40390 Z= 0.272 Chirality : 0.039 0.213 4594 Planarity : 0.004 0.066 5143 Dihedral : 4.743 55.480 4012 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Rotamer: Outliers : 2.50 % Allowed : 14.20 % Favored : 83.30 % 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: 0.26 (0.14), residues: 3559 helix: 1.24 (0.11), residues: 2051 sheet: -2.33 (0.25), residues: 334 loop : -0.85 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1916 HIS 0.007 0.001 HIS A2410 PHE 0.023 0.001 PHE A2421 TYR 0.018 0.001 TYR E 823 ARG 0.003 0.000 ARG A2217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 279 time to evaluate : 3.458 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: symmetry clash REVERT: A 532 LYS cc_start: 0.4065 (OUTLIER) cc_final: 0.3473 (tptp) REVERT: A 548 MET cc_start: 0.4384 (mtt) cc_final: 0.3848 (mmt) REVERT: A 752 GLN cc_start: 0.8434 (mt0) cc_final: 0.8170 (mt0) REVERT: A 772 MET cc_start: 0.8379 (tpt) cc_final: 0.7972 (tpt) REVERT: A 827 MET cc_start: 0.8703 (tmm) cc_final: 0.8072 (tmm) REVERT: A 828 LEU cc_start: 0.9101 (mt) cc_final: 0.8786 (mt) REVERT: A 966 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.7064 (m90) REVERT: A 1151 TYR cc_start: 0.7835 (m-80) cc_final: 0.7501 (m-80) REVERT: A 1467 MET cc_start: 0.8752 (mmm) cc_final: 0.8550 (mmm) REVERT: A 1477 MET cc_start: 0.8528 (tpp) cc_final: 0.8216 (tpp) REVERT: A 1552 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8472 (mm) REVERT: A 1566 LYS cc_start: 0.8687 (ttpt) cc_final: 0.8249 (ttmt) REVERT: A 1809 GLN cc_start: 0.8578 (mt0) cc_final: 0.8237 (tm-30) REVERT: A 2031 LEU cc_start: 0.8735 (mp) cc_final: 0.8369 (tt) REVERT: A 2051 LEU cc_start: 0.8596 (mt) cc_final: 0.8337 (pp) REVERT: A 2161 GLN cc_start: 0.8177 (tm130) cc_final: 0.7801 (tm-30) REVERT: A 2187 LYS cc_start: 0.8683 (mmtp) cc_final: 0.8425 (mmmt) REVERT: A 2199 MET cc_start: 0.8721 (mmt) cc_final: 0.8386 (mmt) REVERT: A 2281 MET cc_start: 0.8732 (mmm) cc_final: 0.8499 (mmm) REVERT: A 2298 ASP cc_start: 0.8182 (m-30) cc_final: 0.7663 (m-30) REVERT: C 100 MET cc_start: 0.8810 (tmm) cc_final: 0.8463 (tmm) REVERT: C 255 MET cc_start: 0.7917 (tpp) cc_final: 0.7588 (tpp) REVERT: E 31 MET cc_start: 0.8641 (ppp) cc_final: 0.7250 (mmt) REVERT: E 33 LYS cc_start: 0.7828 (mmtt) cc_final: 0.7614 (mtpt) REVERT: E 89 ASP cc_start: 0.8832 (t0) cc_final: 0.8308 (t0) REVERT: E 237 MET cc_start: 0.7684 (pmm) cc_final: 0.7192 (pmm) REVERT: E 378 MET cc_start: 0.8863 (mmm) cc_final: 0.8382 (mmm) REVERT: E 431 GLU cc_start: 0.7249 (pt0) cc_final: 0.6975 (tt0) REVERT: E 602 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7740 (mm-30) REVERT: E 961 ASP cc_start: 0.7907 (t70) cc_final: 0.7663 (t70) REVERT: E 1127 MET cc_start: 0.6940 (tpt) cc_final: 0.6589 (mpp) REVERT: E 1131 TRP cc_start: 0.7941 (t-100) cc_final: 0.7697 (t-100) REVERT: E 1276 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.5717 (t80) REVERT: E 1309 PHE cc_start: 0.6219 (m-80) cc_final: 0.5630 (m-10) REVERT: I 370 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7489 (mp10) outliers start: 79 outliers final: 42 residues processed: 338 average time/residue: 0.3916 time to fit residues: 216.1181 Evaluate side-chains 303 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 256 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 940 ASN Chi-restraints excluded: chain A residue 959 PHE Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 968 HIS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1631 GLU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2166 LYS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2501 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 1058 ASP Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1105 ASN Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1236 VAL Chi-restraints excluded: chain E residue 1276 PHE Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 370 GLN Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 145 optimal weight: 0.0010 chunk 300 optimal weight: 0.8980 chunk 243 optimal weight: 0.8980 chunk 0 optimal weight: 50.0000 chunk 179 optimal weight: 7.9990 chunk 315 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29761 Z= 0.178 Angle : 0.551 10.763 40390 Z= 0.266 Chirality : 0.039 0.147 4594 Planarity : 0.004 0.066 5143 Dihedral : 4.658 55.890 4012 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 2.47 % Allowed : 15.05 % Favored : 82.48 % 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: 0.44 (0.14), residues: 3559 helix: 1.38 (0.11), residues: 2058 sheet: -2.21 (0.26), residues: 333 loop : -0.82 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1916 HIS 0.006 0.001 HIS C 161 PHE 0.020 0.001 PHE A2421 TYR 0.028 0.001 TYR E 605 ARG 0.004 0.000 ARG E1012 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 265 time to evaluate : 3.402 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 532 LYS cc_start: 0.4135 (OUTLIER) cc_final: 0.3538 (tptp) REVERT: A 548 MET cc_start: 0.4223 (mtt) cc_final: 0.3596 (mmt) REVERT: A 718 LEU cc_start: 0.5385 (OUTLIER) cc_final: 0.5018 (tp) REVERT: A 752 GLN cc_start: 0.8432 (mt0) cc_final: 0.8222 (mt0) REVERT: A 766 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7981 (ptt180) REVERT: A 827 MET cc_start: 0.8661 (tmm) cc_final: 0.8184 (tmm) REVERT: A 828 LEU cc_start: 0.9173 (mt) cc_final: 0.8889 (mp) REVERT: A 966 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.7087 (m90) REVERT: A 970 MET cc_start: 0.8034 (mtp) cc_final: 0.7758 (mtm) REVERT: A 1467 MET cc_start: 0.8786 (mmm) cc_final: 0.8524 (mmm) REVERT: A 1477 MET cc_start: 0.8508 (tpp) cc_final: 0.8203 (tpp) REVERT: A 1546 TYR cc_start: 0.8221 (m-80) cc_final: 0.7919 (m-80) REVERT: A 1552 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8465 (mm) REVERT: A 1809 GLN cc_start: 0.8570 (mt0) cc_final: 0.8247 (tm-30) REVERT: A 2031 LEU cc_start: 0.8689 (mp) cc_final: 0.8319 (tt) REVERT: A 2051 LEU cc_start: 0.8603 (mt) cc_final: 0.8232 (pp) REVERT: A 2118 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8301 (pp) REVERT: A 2161 GLN cc_start: 0.8151 (tm130) cc_final: 0.7823 (tm-30) REVERT: A 2199 MET cc_start: 0.8706 (mmt) cc_final: 0.8379 (mmt) REVERT: A 2298 ASP cc_start: 0.8160 (m-30) cc_final: 0.7649 (m-30) REVERT: C 100 MET cc_start: 0.8724 (tmm) cc_final: 0.8272 (tmm) REVERT: C 255 MET cc_start: 0.7973 (tpp) cc_final: 0.7595 (tpp) REVERT: E 33 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7606 (mtpt) REVERT: E 72 PRO cc_start: 0.6398 (Cg_exo) cc_final: 0.6078 (Cg_endo) REVERT: E 89 ASP cc_start: 0.8829 (t0) cc_final: 0.8439 (t0) REVERT: E 237 MET cc_start: 0.7444 (pmm) cc_final: 0.7180 (pmm) REVERT: E 411 GLU cc_start: 0.2345 (OUTLIER) cc_final: 0.1713 (tm-30) REVERT: E 431 GLU cc_start: 0.7231 (pt0) cc_final: 0.6976 (pt0) REVERT: E 961 ASP cc_start: 0.7867 (t70) cc_final: 0.7627 (t70) REVERT: E 1088 THR cc_start: 0.4087 (OUTLIER) cc_final: 0.3760 (p) REVERT: E 1127 MET cc_start: 0.6905 (tpt) cc_final: 0.6627 (mpp) REVERT: E 1156 MET cc_start: 0.7068 (mmm) cc_final: 0.6353 (mmt) REVERT: E 1309 PHE cc_start: 0.6243 (m-80) cc_final: 0.5606 (m-10) outliers start: 78 outliers final: 50 residues processed: 319 average time/residue: 0.4133 time to fit residues: 216.5230 Evaluate side-chains 310 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 252 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 940 ASN Chi-restraints excluded: chain A residue 959 PHE Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 968 HIS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1631 GLU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2166 LYS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2501 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 538 ILE Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 685 PHE Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1105 ASN Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 0.0050 chunk 316 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 206 optimal weight: 0.0000 chunk 86 optimal weight: 2.9990 chunk 352 optimal weight: 0.1980 chunk 292 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 184 optimal weight: 0.8980 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29761 Z= 0.145 Angle : 0.535 11.545 40390 Z= 0.256 Chirality : 0.038 0.150 4594 Planarity : 0.004 0.065 5143 Dihedral : 4.490 56.271 4012 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.27 % Rotamer: Outliers : 2.34 % Allowed : 15.75 % Favored : 81.91 % 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: 0.56 (0.14), residues: 3559 helix: 1.49 (0.12), residues: 2045 sheet: -1.97 (0.26), residues: 333 loop : -0.81 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP E1131 HIS 0.005 0.001 HIS C 161 PHE 0.018 0.001 PHE A2421 TYR 0.040 0.001 TYR A 451 ARG 0.004 0.000 ARG A1585 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7118 Ramachandran restraints generated. 3559 Oldfield, 0 Emsley, 3559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 276 time to evaluate : 3.415 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: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.1269 (mtt) cc_final: 0.1027 (mpp) REVERT: A 532 LYS cc_start: 0.4107 (OUTLIER) cc_final: 0.3533 (tptp) REVERT: A 718 LEU cc_start: 0.5322 (OUTLIER) cc_final: 0.4935 (tp) REVERT: A 752 GLN cc_start: 0.8419 (mt0) cc_final: 0.8216 (mt0) REVERT: A 766 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7979 (ptt180) REVERT: A 827 MET cc_start: 0.8573 (tmm) cc_final: 0.8204 (tmm) REVERT: A 966 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.7157 (m90) REVERT: A 970 MET cc_start: 0.8008 (mtp) cc_final: 0.7738 (mtm) REVERT: A 1071 LEU cc_start: 0.9297 (tp) cc_final: 0.9059 (tp) REVERT: A 1078 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.8010 (mtm) REVERT: A 1151 TYR cc_start: 0.7800 (m-80) cc_final: 0.7417 (m-80) REVERT: A 1467 MET cc_start: 0.8748 (mmm) cc_final: 0.8499 (mmm) REVERT: A 1477 MET cc_start: 0.8502 (tpp) cc_final: 0.8176 (tpp) REVERT: A 1546 TYR cc_start: 0.8145 (m-80) cc_final: 0.7906 (m-80) REVERT: A 1552 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8455 (mm) REVERT: A 1809 GLN cc_start: 0.8577 (mt0) cc_final: 0.8236 (tm-30) REVERT: A 2031 LEU cc_start: 0.8696 (mp) cc_final: 0.8329 (tt) REVERT: A 2051 LEU cc_start: 0.8533 (mt) cc_final: 0.8185 (pp) REVERT: A 2118 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8338 (pp) REVERT: A 2161 GLN cc_start: 0.8160 (tm130) cc_final: 0.7913 (tm-30) REVERT: A 2199 MET cc_start: 0.8687 (mmt) cc_final: 0.8375 (mmt) REVERT: A 2281 MET cc_start: 0.8693 (mmm) cc_final: 0.8391 (mmm) REVERT: A 2298 ASP cc_start: 0.8107 (m-30) cc_final: 0.7569 (m-30) REVERT: C 84 VAL cc_start: 0.7298 (OUTLIER) cc_final: 0.6890 (m) REVERT: C 100 MET cc_start: 0.8609 (tmm) cc_final: 0.8286 (ppp) REVERT: C 255 MET cc_start: 0.8007 (tpp) cc_final: 0.7598 (tpp) REVERT: C 273 MET cc_start: 0.7371 (ttp) cc_final: 0.6995 (ttp) REVERT: E 31 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.7419 (mmt) REVERT: E 33 LYS cc_start: 0.7811 (mmtt) cc_final: 0.7578 (mtpt) REVERT: E 72 PRO cc_start: 0.6399 (Cg_exo) cc_final: 0.6098 (Cg_endo) REVERT: E 89 ASP cc_start: 0.8763 (t0) cc_final: 0.8293 (t0) REVERT: E 431 GLU cc_start: 0.7222 (pt0) cc_final: 0.6984 (pt0) REVERT: E 457 LEU cc_start: 0.9326 (mt) cc_final: 0.9112 (mt) REVERT: E 602 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7565 (mm-30) REVERT: E 961 ASP cc_start: 0.7867 (t70) cc_final: 0.7632 (t70) REVERT: E 1008 LYS cc_start: 0.7720 (mttt) cc_final: 0.7317 (tttt) REVERT: E 1088 THR cc_start: 0.4392 (OUTLIER) cc_final: 0.4057 (p) REVERT: E 1156 MET cc_start: 0.6879 (mmm) cc_final: 0.6338 (mmt) REVERT: E 1276 PHE cc_start: 0.6257 (OUTLIER) cc_final: 0.5483 (t80) REVERT: I 328 ARG cc_start: 0.7746 (tmm160) cc_final: 0.7496 (tmm-80) outliers start: 74 outliers final: 44 residues processed: 333 average time/residue: 0.3931 time to fit residues: 214.0401 Evaluate side-chains 317 residues out of total 3164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 262 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain A residue 959 PHE Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 968 HIS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1631 GLU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1895 SER Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2344 LEU Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain A residue 2501 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 170 ASN Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 664 VAL Chi-restraints excluded: chain E residue 1085 LEU Chi-restraints excluded: chain E residue 1088 THR Chi-restraints excluded: chain E residue 1105 ASN Chi-restraints excluded: chain E residue 1166 ASP Chi-restraints excluded: chain E residue 1199 LEU Chi-restraints excluded: chain E residue 1205 MET Chi-restraints excluded: chain E residue 1276 PHE Chi-restraints excluded: chain E residue 1323 TYR Chi-restraints excluded: chain I residue 347 SER Chi-restraints excluded: chain I residue 370 GLN Chi-restraints excluded: chain I residue 407 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.6427 > 50: distance: 48 - 72: 4.517 distance: 52 - 80: 4.708 distance: 59 - 62: 3.728 distance: 61 - 89: 8.373 distance: 62 - 63: 4.108 distance: 63 - 64: 3.723 distance: 64 - 65: 11.210 distance: 65 - 66: 10.688 distance: 67 - 68: 3.394 distance: 69 - 70: 3.645 distance: 69 - 72: 3.929 distance: 70 - 96: 17.011 distance: 75 - 104: 3.491 distance: 76 - 77: 3.131 distance: 77 - 79: 3.888 distance: 81 - 84: 3.121 distance: 82 - 83: 3.843 distance: 83 - 108: 5.917 distance: 90 - 91: 3.612 distance: 90 - 93: 5.476 distance: 91 - 92: 8.033 distance: 91 - 96: 16.150 distance: 92 - 113: 4.953 distance: 93 - 95: 3.878 distance: 96 - 97: 23.495 distance: 97 - 100: 14.871 distance: 98 - 99: 6.864 distance: 98 - 104: 3.628 distance: 99 - 121: 4.887 distance: 100 - 101: 18.273 distance: 100 - 102: 20.507 distance: 101 - 103: 15.264 distance: 105 - 106: 6.038 distance: 106 - 107: 3.917 distance: 107 - 129: 6.258 distance: 108 - 109: 4.281 distance: 109 - 112: 4.301 distance: 110 - 113: 4.027 distance: 111 - 136: 5.313 distance: 113 - 114: 4.013 distance: 114 - 115: 3.914 distance: 115 - 121: 3.148 distance: 116 - 145: 6.341 distance: 117 - 118: 5.328 distance: 118 - 119: 5.568 distance: 118 - 120: 9.061 distance: 122 - 123: 3.403 distance: 122 - 125: 3.581 distance: 124 - 154: 5.975 distance: 125 - 126: 6.217 distance: 126 - 127: 3.244 distance: 126 - 128: 10.070