Starting phenix.real_space_refine on Wed Mar 4 22:15:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uvl_26813/03_2026/7uvl_26813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uvl_26813/03_2026/7uvl_26813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uvl_26813/03_2026/7uvl_26813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uvl_26813/03_2026/7uvl_26813.map" model { file = "/net/cci-nas-00/data/ceres_data/7uvl_26813/03_2026/7uvl_26813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uvl_26813/03_2026/7uvl_26813.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.008 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 10408 2.51 5 N 2808 2.21 5 O 3242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16508 Number of models: 1 Model: "" Number of chains: 5 Chain: "P" Number of atoms: 10254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10254 Classifications: {'peptide': 1285} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 30, 'TRANS': 1254} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1435 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 17, 'TRANS': 191} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 10, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 102 Chain: "A" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1435 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 17, 'TRANS': 191} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 10, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 102 Chain: "L" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1675 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 205} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1709 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 18, 'TRANS': 213} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Residues with excluded nonbonded symmetry interactions: 42 residue: pdb=" N SER L 7 " occ=0.40 ... (4 atoms not shown) pdb=" OG SER L 7 " occ=0.40 residue: pdb=" N THR L 14 " occ=0.60 ... (5 atoms not shown) pdb=" CG2 THR L 14 " occ=0.60 residue: pdb=" N SER L 22 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER L 22 " occ=0.70 residue: pdb=" N GLU L 39 " occ=0.60 ... (7 atoms not shown) pdb=" OE2 GLU L 39 " occ=0.60 residue: pdb=" N SER L 61 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER L 61 " occ=0.70 residue: pdb=" N SER L 68 " occ=0.60 ... (4 atoms not shown) pdb=" OG SER L 68 " occ=0.60 residue: pdb=" N MET L 94 " occ=0.60 ... (6 atoms not shown) pdb=" CE MET L 94 " occ=0.60 residue: pdb=" N ASN L 96 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN L 96 " occ=0.50 residue: pdb=" N LEU L 109 " occ=0.70 ... (6 atoms not shown) pdb=" CD2 LEU L 109 " occ=0.70 residue: pdb=" N LYS L 112 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS L 112 " occ=0.50 residue: pdb=" N SER L 119 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER L 119 " occ=0.70 residue: pdb=" N ASP L 127 " occ=0.60 ... (6 atoms not shown) pdb=" OD2 ASP L 127 " occ=0.60 ... (remaining 30 not shown) Time building chain proxies: 3.32, per 1000 atoms: 0.20 Number of scatterers: 16508 At special positions: 0 Unit cell: (85.012, 139.548, 199.698, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 3242 8.00 N 2808 7.00 C 10408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 196 " - pdb=" SG CYS H 220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 723.6 milliseconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4032 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 32 sheets defined 24.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'P' and resid 1025 through 1036 Processing helix chain 'P' and resid 1332 through 1336 removed outlier: 3.519A pdb=" N ASN P1336 " --> pdb=" O PRO P1333 " (cutoff:3.500A) Processing helix chain 'P' and resid 1362 through 1373 removed outlier: 4.022A pdb=" N LYS P1371 " --> pdb=" O LYS P1367 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU P1372 " --> pdb=" O ASN P1368 " (cutoff:3.500A) Processing helix chain 'P' and resid 1377 through 1387 Processing helix chain 'P' and resid 1392 through 1396 removed outlier: 4.054A pdb=" N TYR P1395 " --> pdb=" O ASN P1392 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR P1396 " --> pdb=" O THR P1393 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 1392 through 1396' Processing helix chain 'P' and resid 1412 through 1417 Processing helix chain 'P' and resid 1468 through 1481 removed outlier: 4.841A pdb=" N ASN P1477 " --> pdb=" O LYS P1473 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ASP P1478 " --> pdb=" O ALA P1474 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER P1481 " --> pdb=" O ASN P1477 " (cutoff:3.500A) Processing helix chain 'P' and resid 1486 through 1493 removed outlier: 3.878A pdb=" N ARG P1490 " --> pdb=" O SER P1486 " (cutoff:3.500A) Processing helix chain 'P' and resid 1506 through 1516 Processing helix chain 'P' and resid 1516 through 1529 removed outlier: 3.631A pdb=" N SER P1520 " --> pdb=" O ASN P1516 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA P1529 " --> pdb=" O LEU P1525 " (cutoff:3.500A) Processing helix chain 'P' and resid 1537 through 1550 removed outlier: 3.662A pdb=" N ASN P1550 " --> pdb=" O LYS P1546 " (cutoff:3.500A) Processing helix chain 'P' and resid 1550 through 1565 Processing helix chain 'P' and resid 1574 through 1580 Processing helix chain 'P' and resid 1581 through 1585 removed outlier: 4.310A pdb=" N PHE P1585 " --> pdb=" O LEU P1582 " (cutoff:3.500A) Processing helix chain 'P' and resid 1591 through 1601 Processing helix chain 'P' and resid 1603 through 1608 Processing helix chain 'P' and resid 1611 through 1619 Processing helix chain 'P' and resid 1628 through 1640 Processing helix chain 'P' and resid 1645 through 1654 Processing helix chain 'P' and resid 1665 through 1674 removed outlier: 3.722A pdb=" N LYS P1674 " --> pdb=" O SER P1670 " (cutoff:3.500A) Processing helix chain 'P' and resid 1682 through 1689 Processing helix chain 'P' and resid 1694 through 1699 removed outlier: 3.765A pdb=" N MET P1697 " --> pdb=" O TYR P1694 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL P1698 " --> pdb=" O GLN P1695 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU P1699 " --> pdb=" O SER P1696 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 1694 through 1699' Processing helix chain 'P' and resid 1724 through 1728 removed outlier: 3.586A pdb=" N ARG P1728 " --> pdb=" O TYR P1724 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 1724 through 1728' Processing helix chain 'P' and resid 1735 through 1764 Processing helix chain 'P' and resid 1768 through 1774 removed outlier: 4.093A pdb=" N PHE P1773 " --> pdb=" O GLU P1770 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG P1774 " --> pdb=" O LYS P1771 " (cutoff:3.500A) Processing helix chain 'P' and resid 1801 through 1807 Processing helix chain 'P' and resid 1838 through 1853 Processing helix chain 'P' and resid 1910 through 1915 removed outlier: 3.834A pdb=" N PHE P1915 " --> pdb=" O PRO P1911 " (cutoff:3.500A) Processing helix chain 'P' and resid 1917 through 1945 removed outlier: 3.870A pdb=" N LYS P1945 " --> pdb=" O ARG P1941 " (cutoff:3.500A) Processing helix chain 'P' and resid 1947 through 1954 Processing helix chain 'P' and resid 1981 through 1988 Processing helix chain 'P' and resid 1990 through 1998 removed outlier: 3.821A pdb=" N LEU P1994 " --> pdb=" O SER P1990 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE P1995 " --> pdb=" O PHE P1991 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU P1996 " --> pdb=" O ASP P1992 " (cutoff:3.500A) Processing helix chain 'P' and resid 2038 through 2052 Processing helix chain 'P' and resid 2066 through 2074 Processing helix chain 'P' and resid 2088 through 2097 Processing helix chain 'P' and resid 2103 through 2122 Processing helix chain 'P' and resid 2144 through 2160 removed outlier: 4.044A pdb=" N LEU P2148 " --> pdb=" O ASN P2144 " (cutoff:3.500A) Processing helix chain 'P' and resid 2173 through 2190 removed outlier: 3.545A pdb=" N LYS P2177 " --> pdb=" O SER P2173 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 311 through 317 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 420 through 427 removed outlier: 3.971A pdb=" N TRP B 424 " --> pdb=" O ALA B 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 311 through 318 Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.516A pdb=" N ASN A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.941A pdb=" N TRP A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 188 through 194 Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'H' and resid 193 through 198 Processing sheet with id=AA1, first strand: chain 'P' and resid 928 through 931 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 928 through 931 current: chain 'P' and resid 942 through 943 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 942 through 943 current: chain 'P' and resid 969 through 979 removed outlier: 4.012A pdb=" N SER P 975 " --> pdb=" O VAL P 990 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR P 987 " --> pdb=" O LEU P1012 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 998 through 1000 Processing sheet with id=AA3, first strand: chain 'P' and resid 1040 through 1042 removed outlier: 6.959A pdb=" N ILE P1071 " --> pdb=" O GLN P1098 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 1096 through 1098 current: chain 'P' and resid 1152 through 1164 removed outlier: 8.796A pdb=" N THR P1152 " --> pdb=" O ILE P1188 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N LYS P1190 " --> pdb=" O THR P1152 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N SER P1154 " --> pdb=" O LYS P1190 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ILE P1192 " --> pdb=" O SER P1154 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER P1156 " --> pdb=" O ILE P1192 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N SER P1194 " --> pdb=" O SER P1156 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE P1158 " --> pdb=" O SER P1194 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP P1196 " --> pdb=" O PHE P1158 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY P1160 " --> pdb=" O ASP P1196 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ALA P1198 " --> pdb=" O GLY P1160 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE P1162 " --> pdb=" O ALA P1198 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE P1188 " --> pdb=" O THR P1220 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 1220 through 1222 current: chain 'P' and resid 1288 through 1290 Processing sheet with id=AA4, first strand: chain 'P' and resid 1047 through 1048 removed outlier: 7.143A pdb=" N MET P1047 " --> pdb=" O TYR P1082 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'P' and resid 1092 through 1093 removed outlier: 8.011A pdb=" N LEU P1092 " --> pdb=" O LYS P1121 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS P1118 " --> pdb=" O GLN P1147 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER P1146 " --> pdb=" O VAL P1178 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLY P1179 " --> pdb=" O VAL P1214 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASP P1216 " --> pdb=" O GLY P1179 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU P1181 " --> pdb=" O ASP P1216 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLY P1213 " --> pdb=" O VAL P1243 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN P1245 " --> pdb=" O GLY P1213 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL P1215 " --> pdb=" O ASN P1245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 1112 through 1114 Processing sheet with id=AA7, first strand: chain 'P' and resid 1173 through 1175 removed outlier: 6.271A pdb=" N VAL P1208 " --> pdb=" O GLY P1240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 1398 through 1402 removed outlier: 4.987A pdb=" N HIS P1427 " --> pdb=" O LEU P1399 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER P1401 " --> pdb=" O LEU P1425 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU P1425 " --> pdb=" O SER P1401 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN P1434 " --> pdb=" O LEU P1426 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 1439 through 1440 removed outlier: 3.613A pdb=" N LEU P1457 " --> pdb=" O ILE P1452 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 1568 through 1569 Processing sheet with id=AB2, first strand: chain 'P' and resid 1657 through 1659 removed outlier: 6.462A pdb=" N TYR P1657 " --> pdb=" O MET P1712 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ALA P1714 " --> pdb=" O TYR P1657 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL P1659 " --> pdb=" O ALA P1714 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU P1777 " --> pdb=" O PHE P1829 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR P1830 " --> pdb=" O TYR P1823 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR P1823 " --> pdb=" O TYR P1830 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 1999 through 2001 removed outlier: 3.982A pdb=" N ASN P1975 " --> pdb=" O TYR P2011 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 2077 through 2079 Processing sheet with id=AB5, first strand: chain 'B' and resid 245 through 249 removed outlier: 3.754A pdb=" N THR B 265 " --> pdb=" O HIS B 249 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 264 through 271 current: chain 'B' and resid 302 through 308 Processing sheet with id=AB6, first strand: chain 'B' and resid 278 through 281 removed outlier: 5.526A pdb=" N TYR B 327 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR B 332 " --> pdb=" O TYR B 327 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 348 through 352 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 365 through 374 current: chain 'B' and resid 411 through 419 Processing sheet with id=AB8, first strand: chain 'B' and resid 388 through 389 removed outlier: 4.045A pdb=" N PHE B 430 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE B 448 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 245 through 249 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 264 through 271 current: chain 'A' and resid 302 through 308 Processing sheet with id=AC1, first strand: chain 'A' and resid 278 through 281 removed outlier: 5.306A pdb=" N TYR A 327 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N THR A 332 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 348 through 352 removed outlier: 6.088A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 388 through 389 removed outlier: 3.947A pdb=" N PHE A 430 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 448 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A 446 " --> pdb=" O CYS A 432 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.894A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.337A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'L' and resid 19 through 21 Processing sheet with id=AC7, first strand: chain 'L' and resid 50 through 51 removed outlier: 3.527A pdb=" N MET L 94 " --> pdb=" O GLU L 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 120 through 123 removed outlier: 5.644A pdb=" N SER L 136 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU L 186 " --> pdb=" O SER L 136 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL L 138 " --> pdb=" O LEU L 184 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU L 184 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU L 140 " --> pdb=" O SER L 182 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N SER L 182 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASN L 142 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU L 180 " --> pdb=" O ASN L 142 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN L 165 " --> pdb=" O THR L 183 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.638A pdb=" N TRP L 153 " --> pdb=" O GLN L 160 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 196 through 198 Processing sheet with id=AD2, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 60 through 62 removed outlier: 3.834A pdb=" N ALA H 61 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG H 50 " --> pdb=" O ALA H 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 126 through 128 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 140 through 150 current: chain 'H' and resid 183 through 192 Processing sheet with id=AD5, first strand: chain 'H' and resid 158 through 159 481 hydrogen bonds defined for protein. 1311 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: 4.58 Time building geometry restraints manager: 1.62 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: 5430 1.34 - 1.46: 3800 1.46 - 1.58: 7536 1.58 - 1.70: 0 1.70 - 1.81: 76 Bond restraints: 16842 Sorted by residual: bond pdb=" C GLU H 154 " pdb=" N PRO H 155 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.79e+00 bond pdb=" C LYS P1086 " pdb=" N PRO P1087 " ideal model delta sigma weight residual 1.331 1.348 -0.017 1.27e-02 6.20e+03 1.78e+00 bond pdb=" C ASN P 953 " pdb=" N PRO P 954 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.54e+00 bond pdb=" C THR A 282 " pdb=" N PRO A 283 " ideal model delta sigma weight residual 1.340 1.371 -0.031 2.76e-02 1.31e+03 1.27e+00 bond pdb=" N LYS P1456 " pdb=" CA LYS P1456 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.19e+00 ... (remaining 16837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 22431 1.68 - 3.36: 398 3.36 - 5.04: 45 5.04 - 6.72: 12 6.72 - 8.40: 3 Bond angle restraints: 22889 Sorted by residual: angle pdb=" C GLN P2118 " pdb=" N PHE P2119 " pdb=" CA PHE P2119 " ideal model delta sigma weight residual 121.14 115.13 6.01 1.75e+00 3.27e-01 1.18e+01 angle pdb=" N PHE P2119 " pdb=" CA PHE P2119 " pdb=" CB PHE P2119 " ideal model delta sigma weight residual 110.40 115.31 -4.91 1.63e+00 3.76e-01 9.06e+00 angle pdb=" CB MET P2044 " pdb=" CG MET P2044 " pdb=" SD MET P2044 " ideal model delta sigma weight residual 112.70 121.10 -8.40 3.00e+00 1.11e-01 7.85e+00 angle pdb=" CB MET P2040 " pdb=" CG MET P2040 " pdb=" SD MET P2040 " ideal model delta sigma weight residual 112.70 121.04 -8.34 3.00e+00 1.11e-01 7.72e+00 angle pdb=" N ASN P1343 " pdb=" CA ASN P1343 " pdb=" C ASN P1343 " ideal model delta sigma weight residual 108.14 112.33 -4.19 1.52e+00 4.33e-01 7.61e+00 ... (remaining 22884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 9309 17.50 - 35.00: 711 35.00 - 52.50: 110 52.50 - 70.01: 20 70.01 - 87.51: 11 Dihedral angle restraints: 10161 sinusoidal: 3887 harmonic: 6274 Sorted by residual: dihedral pdb=" CA GLU H 154 " pdb=" C GLU H 154 " pdb=" N PRO H 155 " pdb=" CA PRO H 155 " ideal model delta harmonic sigma weight residual -180.00 -147.42 -32.58 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CB CYS L 139 " pdb=" SG CYS L 139 " pdb=" SG CYS L 199 " pdb=" CB CYS L 199 " ideal model delta sinusoidal sigma weight residual 93.00 46.40 46.60 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA TYR H 97 " pdb=" C TYR H 97 " pdb=" N CYS H 98 " pdb=" CA CYS H 98 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 10158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2233 0.056 - 0.112: 334 0.112 - 0.168: 39 0.168 - 0.224: 1 0.224 - 0.280: 1 Chirality restraints: 2608 Sorted by residual: chirality pdb=" CB VAL P1475 " pdb=" CA VAL P1475 " pdb=" CG1 VAL P1475 " pdb=" CG2 VAL P1475 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ASN P 953 " pdb=" N ASN P 953 " pdb=" C ASN P 953 " pdb=" CB ASN P 953 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CA PRO H 155 " pdb=" N PRO H 155 " pdb=" C PRO H 155 " pdb=" CB PRO H 155 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.06e-01 ... (remaining 2605 not shown) Planarity restraints: 2965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 154 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO H 155 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO H 155 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 155 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS H 220 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO H 221 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO H 221 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 221 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H 136 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO H 137 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO H 137 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 137 " -0.024 5.00e-02 4.00e+02 ... (remaining 2962 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 574 2.71 - 3.26: 17423 3.26 - 3.80: 27519 3.80 - 4.35: 34294 4.35 - 4.90: 56872 Nonbonded interactions: 136682 Sorted by model distance: nonbonded pdb=" OH TYR P1172 " pdb=" O ASN P1200 " model vdw 2.161 3.040 nonbonded pdb=" O VAL P2059 " pdb=" OG SER P2063 " model vdw 2.183 3.040 nonbonded pdb=" O GLU P1330 " pdb=" NZ LYS P1334 " model vdw 2.202 3.120 nonbonded pdb=" OH TYR P1962 " pdb=" OG SER P2031 " model vdw 2.211 3.040 nonbonded pdb=" OD1 ASN P1566 " pdb=" NZ LYS P1575 " model vdw 2.212 3.120 ... (remaining 136677 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=0.99 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: 8.170 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.060 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 0.003 0.045 16851 Z= 0.125 Angle : 0.563 8.405 22907 Z= 0.305 Chirality : 0.041 0.280 2608 Planarity : 0.004 0.044 2965 Dihedral : 12.922 87.507 6102 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.18), residues: 2142 helix: 0.81 (0.25), residues: 475 sheet: 0.23 (0.23), residues: 515 loop : -1.34 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 113 TYR 0.015 0.001 TYR P1924 PHE 0.018 0.001 PHE P2193 TRP 0.012 0.001 TRP H 109 HIS 0.005 0.001 HIS P1847 Details of bonding type rmsd covalent geometry : bond 0.00271 (16842) covalent geometry : angle 0.56298 (22889) SS BOND : bond 0.00193 ( 9) SS BOND : angle 0.56683 ( 18) hydrogen bonds : bond 0.22117 ( 481) hydrogen bonds : angle 8.51960 ( 1311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: P 1038 TYR cc_start: 0.8822 (t80) cc_final: 0.8592 (t80) REVERT: P 1832 MET cc_start: 0.8251 (mmm) cc_final: 0.7822 (mmm) REVERT: L 94 MET cc_start: 0.6872 (ppp) cc_final: 0.6348 (ppp) REVERT: H 36 TRP cc_start: 0.6465 (m-90) cc_final: 0.5086 (m-90) REVERT: H 82 PHE cc_start: 0.9426 (m-10) cc_final: 0.9079 (m-80) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1173 time to fit residues: 13.7773 Evaluate side-chains 50 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.5980 chunk 77 optimal weight: 0.0030 chunk 122 optimal weight: 0.3980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1322 ASN P1672 GLN P1745 ASN ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P2020 ASN ** P2131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS L 160 GLN ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.067723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.044755 restraints weight = 97064.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.046305 restraints weight = 44785.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.047282 restraints weight = 28112.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.047789 restraints weight = 21166.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.048297 restraints weight = 18029.832| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16851 Z= 0.114 Angle : 0.551 7.739 22907 Z= 0.292 Chirality : 0.042 0.169 2608 Planarity : 0.004 0.047 2965 Dihedral : 4.653 34.233 2318 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.28 % Allowed : 6.27 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.18), residues: 2142 helix: 0.85 (0.24), residues: 481 sheet: 0.25 (0.22), residues: 527 loop : -1.36 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 113 TYR 0.028 0.001 TYR P1348 PHE 0.040 0.001 PHE P2119 TRP 0.008 0.001 TRP A 424 HIS 0.003 0.001 HIS H 208 Details of bonding type rmsd covalent geometry : bond 0.00254 (16842) covalent geometry : angle 0.55098 (22889) SS BOND : bond 0.00299 ( 9) SS BOND : angle 0.62787 ( 18) hydrogen bonds : bond 0.04378 ( 481) hydrogen bonds : angle 6.33943 ( 1311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.624 Fit side-chains REVERT: P 1832 MET cc_start: 0.8189 (mmm) cc_final: 0.7818 (mmm) REVERT: H 82 PHE cc_start: 0.9389 (m-10) cc_final: 0.9183 (m-80) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.1140 time to fit residues: 12.2338 Evaluate side-chains 55 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1455 THR Chi-restraints excluded: chain P residue 2170 ASP Chi-restraints excluded: chain L residue 35 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 191 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 152 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1927 ASN ** P2131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.067097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.044765 restraints weight = 98444.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.046570 restraints weight = 49950.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.046564 restraints weight = 27558.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.046791 restraints weight = 27791.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.046878 restraints weight = 24241.323| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16851 Z= 0.108 Angle : 0.522 12.296 22907 Z= 0.273 Chirality : 0.041 0.160 2608 Planarity : 0.003 0.047 2965 Dihedral : 4.532 34.047 2318 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.45 % Allowed : 8.52 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 2142 helix: 1.02 (0.24), residues: 476 sheet: 0.28 (0.22), residues: 517 loop : -1.33 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 113 TYR 0.014 0.001 TYR H 97 PHE 0.034 0.001 PHE P2119 TRP 0.010 0.001 TRP H 109 HIS 0.004 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00246 (16842) covalent geometry : angle 0.52229 (22889) SS BOND : bond 0.00264 ( 9) SS BOND : angle 0.58295 ( 18) hydrogen bonds : bond 0.03796 ( 481) hydrogen bonds : angle 5.65906 ( 1311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: P 1047 MET cc_start: 0.6447 (tpp) cc_final: 0.6065 (tpp) REVERT: P 1832 MET cc_start: 0.8049 (mmm) cc_final: 0.7710 (mmm) REVERT: P 1849 MET cc_start: 0.9418 (OUTLIER) cc_final: 0.9148 (mmp) REVERT: H 82 PHE cc_start: 0.9261 (m-10) cc_final: 0.9032 (m-80) outliers start: 8 outliers final: 3 residues processed: 65 average time/residue: 0.1141 time to fit residues: 12.3617 Evaluate side-chains 58 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1382 VAL Chi-restraints excluded: chain P residue 1455 THR Chi-restraints excluded: chain P residue 1849 MET Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 101 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 133 optimal weight: 0.0000 chunk 162 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 172 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 999 HIS P1581 HIS ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.066055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.042500 restraints weight = 97703.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.043969 restraints weight = 46333.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.044858 restraints weight = 29726.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.045470 restraints weight = 22717.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.045764 restraints weight = 19193.543| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16851 Z= 0.163 Angle : 0.557 11.365 22907 Z= 0.288 Chirality : 0.041 0.161 2608 Planarity : 0.004 0.047 2965 Dihedral : 4.610 40.481 2318 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.18 % Allowed : 10.14 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.18), residues: 2142 helix: 1.00 (0.24), residues: 482 sheet: 0.27 (0.22), residues: 516 loop : -1.36 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 113 TYR 0.032 0.002 TYR P1348 PHE 0.032 0.002 PHE P2119 TRP 0.016 0.001 TRP H 109 HIS 0.004 0.001 HIS P1847 Details of bonding type rmsd covalent geometry : bond 0.00373 (16842) covalent geometry : angle 0.55673 (22889) SS BOND : bond 0.00257 ( 9) SS BOND : angle 0.57612 ( 18) hydrogen bonds : bond 0.03762 ( 481) hydrogen bonds : angle 5.40019 ( 1311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 1849 MET cc_start: 0.9508 (OUTLIER) cc_final: 0.9213 (mmp) REVERT: L 48 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.9096 (t) outliers start: 21 outliers final: 9 residues processed: 72 average time/residue: 0.1161 time to fit residues: 14.0283 Evaluate side-chains 64 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1178 VAL Chi-restraints excluded: chain P residue 1382 VAL Chi-restraints excluded: chain P residue 1455 THR Chi-restraints excluded: chain P residue 1732 TYR Chi-restraints excluded: chain P residue 1778 VAL Chi-restraints excluded: chain P residue 1849 MET Chi-restraints excluded: chain P residue 1985 ILE Chi-restraints excluded: chain P residue 2125 VAL Chi-restraints excluded: chain P residue 2170 ASP Chi-restraints excluded: chain L residue 48 SER Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 207 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 175 optimal weight: 20.0000 chunk 210 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 999 HIS P1007 ASN ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.065934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.042362 restraints weight = 97742.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.043847 restraints weight = 46536.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.044770 restraints weight = 29780.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.045351 restraints weight = 22615.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.045667 restraints weight = 19154.546| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16851 Z= 0.155 Angle : 0.550 10.348 22907 Z= 0.286 Chirality : 0.041 0.162 2608 Planarity : 0.003 0.046 2965 Dihedral : 4.623 41.961 2318 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.57 % Allowed : 11.43 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.18), residues: 2142 helix: 1.08 (0.24), residues: 476 sheet: 0.16 (0.22), residues: 535 loop : -1.37 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 50 TYR 0.013 0.001 TYR P1010 PHE 0.030 0.001 PHE P2119 TRP 0.009 0.001 TRP P2134 HIS 0.005 0.001 HIS P1581 Details of bonding type rmsd covalent geometry : bond 0.00354 (16842) covalent geometry : angle 0.55015 (22889) SS BOND : bond 0.00240 ( 9) SS BOND : angle 0.64318 ( 18) hydrogen bonds : bond 0.03643 ( 481) hydrogen bonds : angle 5.26343 ( 1311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: P 1047 MET cc_start: 0.5669 (tpp) cc_final: 0.5335 (tpp) REVERT: P 1832 MET cc_start: 0.8152 (mmm) cc_final: 0.7736 (mmm) REVERT: P 1849 MET cc_start: 0.9577 (OUTLIER) cc_final: 0.9321 (mmp) REVERT: P 2019 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8935 (mt) REVERT: L 48 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.9107 (t) outliers start: 28 outliers final: 14 residues processed: 77 average time/residue: 0.1153 time to fit residues: 14.8885 Evaluate side-chains 71 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 944 VAL Chi-restraints excluded: chain P residue 1178 VAL Chi-restraints excluded: chain P residue 1382 VAL Chi-restraints excluded: chain P residue 1455 THR Chi-restraints excluded: chain P residue 1489 VAL Chi-restraints excluded: chain P residue 1732 TYR Chi-restraints excluded: chain P residue 1777 LEU Chi-restraints excluded: chain P residue 1778 VAL Chi-restraints excluded: chain P residue 1849 MET Chi-restraints excluded: chain P residue 1885 TYR Chi-restraints excluded: chain P residue 1985 ILE Chi-restraints excluded: chain P residue 2000 ILE Chi-restraints excluded: chain P residue 2019 ILE Chi-restraints excluded: chain P residue 2125 VAL Chi-restraints excluded: chain P residue 2170 ASP Chi-restraints excluded: chain L residue 48 SER Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 23 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 203 optimal weight: 7.9990 chunk 173 optimal weight: 40.0000 chunk 99 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 998 GLN P 999 HIS ** P1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** H 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.064549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.040649 restraints weight = 97290.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.042013 restraints weight = 48131.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.042889 restraints weight = 31714.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.043396 restraints weight = 24573.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.043712 restraints weight = 21075.577| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16851 Z= 0.252 Angle : 0.643 15.215 22907 Z= 0.334 Chirality : 0.043 0.162 2608 Planarity : 0.004 0.046 2965 Dihedral : 4.980 42.807 2318 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.90 % Allowed : 12.89 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.18), residues: 2142 helix: 0.69 (0.24), residues: 486 sheet: 0.11 (0.22), residues: 522 loop : -1.38 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P2042 TYR 0.033 0.002 TYR P1348 PHE 0.032 0.002 PHE P2119 TRP 0.012 0.002 TRP P2134 HIS 0.010 0.002 HIS P1817 Details of bonding type rmsd covalent geometry : bond 0.00571 (16842) covalent geometry : angle 0.64352 (22889) SS BOND : bond 0.00216 ( 9) SS BOND : angle 0.58872 ( 18) hydrogen bonds : bond 0.04254 ( 481) hydrogen bonds : angle 5.47704 ( 1311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 54 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: P 1047 MET cc_start: 0.6000 (tpp) cc_final: 0.5534 (tpp) REVERT: L 94 MET cc_start: 0.8404 (ppp) cc_final: 0.8132 (ppp) outliers start: 34 outliers final: 24 residues processed: 85 average time/residue: 0.1088 time to fit residues: 15.5118 Evaluate side-chains 76 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 944 VAL Chi-restraints excluded: chain P residue 976 ILE Chi-restraints excluded: chain P residue 1010 TYR Chi-restraints excluded: chain P residue 1033 MET Chi-restraints excluded: chain P residue 1178 VAL Chi-restraints excluded: chain P residue 1382 VAL Chi-restraints excluded: chain P residue 1455 THR Chi-restraints excluded: chain P residue 1475 VAL Chi-restraints excluded: chain P residue 1489 VAL Chi-restraints excluded: chain P residue 1580 TYR Chi-restraints excluded: chain P residue 1641 LEU Chi-restraints excluded: chain P residue 1732 TYR Chi-restraints excluded: chain P residue 1777 LEU Chi-restraints excluded: chain P residue 1778 VAL Chi-restraints excluded: chain P residue 1849 MET Chi-restraints excluded: chain P residue 1885 TYR Chi-restraints excluded: chain P residue 1894 VAL Chi-restraints excluded: chain P residue 1985 ILE Chi-restraints excluded: chain P residue 2000 ILE Chi-restraints excluded: chain P residue 2019 ILE Chi-restraints excluded: chain P residue 2125 VAL Chi-restraints excluded: chain P residue 2170 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 75 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 998 GLN ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.065880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.042237 restraints weight = 96634.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.043714 restraints weight = 45991.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.044573 restraints weight = 29557.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.045185 restraints weight = 22686.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.045476 restraints weight = 19211.219| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16851 Z= 0.116 Angle : 0.545 13.725 22907 Z= 0.284 Chirality : 0.041 0.154 2608 Planarity : 0.003 0.047 2965 Dihedral : 4.751 40.571 2318 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.01 % Allowed : 14.29 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.18), residues: 2142 helix: 1.00 (0.24), residues: 486 sheet: 0.17 (0.22), residues: 534 loop : -1.41 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 50 TYR 0.026 0.001 TYR P1225 PHE 0.031 0.001 PHE P2119 TRP 0.010 0.001 TRP H 109 HIS 0.007 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00266 (16842) covalent geometry : angle 0.54493 (22889) SS BOND : bond 0.00231 ( 9) SS BOND : angle 0.66597 ( 18) hydrogen bonds : bond 0.03552 ( 481) hydrogen bonds : angle 5.05365 ( 1311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 1225 TYR cc_start: 0.5288 (m-10) cc_final: 0.4972 (m-10) REVERT: L 94 MET cc_start: 0.8506 (ppp) cc_final: 0.8223 (ppp) outliers start: 18 outliers final: 13 residues processed: 73 average time/residue: 0.1211 time to fit residues: 14.5159 Evaluate side-chains 69 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1178 VAL Chi-restraints excluded: chain P residue 1455 THR Chi-restraints excluded: chain P residue 1489 VAL Chi-restraints excluded: chain P residue 1732 TYR Chi-restraints excluded: chain P residue 1777 LEU Chi-restraints excluded: chain P residue 1778 VAL Chi-restraints excluded: chain P residue 1817 HIS Chi-restraints excluded: chain P residue 1849 MET Chi-restraints excluded: chain P residue 1885 TYR Chi-restraints excluded: chain P residue 1894 VAL Chi-restraints excluded: chain P residue 2125 VAL Chi-restraints excluded: chain P residue 2170 ASP Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 58 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 199 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 71 optimal weight: 0.0060 chunk 148 optimal weight: 7.9990 chunk 14 optimal weight: 0.0980 overall best weight: 1.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.065478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.041686 restraints weight = 97630.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.043150 restraints weight = 46457.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.044020 restraints weight = 29945.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.044642 restraints weight = 22996.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.044984 restraints weight = 19460.968| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16851 Z= 0.153 Angle : 0.554 13.290 22907 Z= 0.286 Chirality : 0.041 0.155 2608 Planarity : 0.003 0.047 2965 Dihedral : 4.694 41.997 2318 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.40 % Allowed : 14.68 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.18), residues: 2142 helix: 1.01 (0.24), residues: 486 sheet: 0.18 (0.22), residues: 536 loop : -1.40 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P2042 TYR 0.033 0.001 TYR P1348 PHE 0.035 0.002 PHE P2119 TRP 0.009 0.001 TRP H 109 HIS 0.006 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00352 (16842) covalent geometry : angle 0.55421 (22889) SS BOND : bond 0.00211 ( 9) SS BOND : angle 0.57708 ( 18) hydrogen bonds : bond 0.03591 ( 481) hydrogen bonds : angle 4.99647 ( 1311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1047 MET cc_start: 0.5589 (tpp) cc_final: 0.5244 (tpp) REVERT: P 1225 TYR cc_start: 0.5509 (m-10) cc_final: 0.5273 (m-10) outliers start: 25 outliers final: 19 residues processed: 75 average time/residue: 0.1260 time to fit residues: 15.4860 Evaluate side-chains 74 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 944 VAL Chi-restraints excluded: chain P residue 1010 TYR Chi-restraints excluded: chain P residue 1100 LEU Chi-restraints excluded: chain P residue 1178 VAL Chi-restraints excluded: chain P residue 1226 VAL Chi-restraints excluded: chain P residue 1455 THR Chi-restraints excluded: chain P residue 1489 VAL Chi-restraints excluded: chain P residue 1732 TYR Chi-restraints excluded: chain P residue 1777 LEU Chi-restraints excluded: chain P residue 1778 VAL Chi-restraints excluded: chain P residue 1849 MET Chi-restraints excluded: chain P residue 1885 TYR Chi-restraints excluded: chain P residue 1894 VAL Chi-restraints excluded: chain P residue 1918 VAL Chi-restraints excluded: chain P residue 2019 ILE Chi-restraints excluded: chain P residue 2125 VAL Chi-restraints excluded: chain P residue 2170 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 74 optimal weight: 0.7980 chunk 175 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 195 optimal weight: 0.0980 chunk 142 optimal weight: 30.0000 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 0.0870 chunk 160 optimal weight: 6.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1509 GLN ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 GLN ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 GLN ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.066712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.043286 restraints weight = 96989.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.044830 restraints weight = 44660.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.045781 restraints weight = 28168.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.046318 restraints weight = 21273.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.046748 restraints weight = 18052.959| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16851 Z= 0.099 Angle : 0.531 12.049 22907 Z= 0.273 Chirality : 0.040 0.151 2608 Planarity : 0.003 0.046 2965 Dihedral : 4.512 40.592 2318 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.01 % Allowed : 15.18 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 2142 helix: 1.22 (0.24), residues: 480 sheet: 0.27 (0.22), residues: 531 loop : -1.37 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 107 TYR 0.018 0.001 TYR P1225 PHE 0.032 0.001 PHE P2119 TRP 0.009 0.001 TRP P1564 HIS 0.004 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00226 (16842) covalent geometry : angle 0.53105 (22889) SS BOND : bond 0.00231 ( 9) SS BOND : angle 0.70461 ( 18) hydrogen bonds : bond 0.03222 ( 481) hydrogen bonds : angle 4.69980 ( 1311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 2076 LYS cc_start: 0.8452 (mmtt) cc_final: 0.7442 (mmpt) outliers start: 18 outliers final: 16 residues processed: 72 average time/residue: 0.1271 time to fit residues: 14.5682 Evaluate side-chains 73 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 944 VAL Chi-restraints excluded: chain P residue 1100 LEU Chi-restraints excluded: chain P residue 1178 VAL Chi-restraints excluded: chain P residue 1226 VAL Chi-restraints excluded: chain P residue 1455 THR Chi-restraints excluded: chain P residue 1489 VAL Chi-restraints excluded: chain P residue 1659 VAL Chi-restraints excluded: chain P residue 1732 TYR Chi-restraints excluded: chain P residue 1778 VAL Chi-restraints excluded: chain P residue 1849 MET Chi-restraints excluded: chain P residue 1885 TYR Chi-restraints excluded: chain P residue 1894 VAL Chi-restraints excluded: chain P residue 1918 VAL Chi-restraints excluded: chain P residue 2125 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.0870 chunk 181 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 998 GLN ** P 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1206 GLN ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.065014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.041114 restraints weight = 96883.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.042563 restraints weight = 46520.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.043467 restraints weight = 30007.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.043987 restraints weight = 23077.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.044228 restraints weight = 19681.512| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16851 Z= 0.212 Angle : 0.601 13.517 22907 Z= 0.308 Chirality : 0.042 0.157 2608 Planarity : 0.004 0.047 2965 Dihedral : 4.680 41.972 2318 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.95 % Allowed : 15.57 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.18), residues: 2142 helix: 1.05 (0.24), residues: 480 sheet: 0.18 (0.22), residues: 536 loop : -1.35 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P2042 TYR 0.032 0.002 TYR P1348 PHE 0.032 0.002 PHE P2119 TRP 0.010 0.001 TRP P2104 HIS 0.007 0.001 HIS P1581 Details of bonding type rmsd covalent geometry : bond 0.00484 (16842) covalent geometry : angle 0.60085 (22889) SS BOND : bond 0.00226 ( 9) SS BOND : angle 0.65958 ( 18) hydrogen bonds : bond 0.03773 ( 481) hydrogen bonds : angle 4.94942 ( 1311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 1247 TRP cc_start: 0.6372 (t60) cc_final: 0.5747 (t60) REVERT: P 2076 LYS cc_start: 0.8517 (mmtt) cc_final: 0.7509 (mmpt) outliers start: 17 outliers final: 15 residues processed: 69 average time/residue: 0.1253 time to fit residues: 13.9620 Evaluate side-chains 70 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 944 VAL Chi-restraints excluded: chain P residue 1100 LEU Chi-restraints excluded: chain P residue 1178 VAL Chi-restraints excluded: chain P residue 1226 VAL Chi-restraints excluded: chain P residue 1455 THR Chi-restraints excluded: chain P residue 1489 VAL Chi-restraints excluded: chain P residue 1580 TYR Chi-restraints excluded: chain P residue 1732 TYR Chi-restraints excluded: chain P residue 1778 VAL Chi-restraints excluded: chain P residue 1849 MET Chi-restraints excluded: chain P residue 1885 TYR Chi-restraints excluded: chain P residue 1894 VAL Chi-restraints excluded: chain P residue 2125 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 88 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 14 optimal weight: 0.0060 chunk 78 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 125 optimal weight: 0.0570 chunk 160 optimal weight: 8.9990 chunk 154 optimal weight: 20.0000 chunk 190 optimal weight: 0.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.066379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.042858 restraints weight = 95871.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.044315 restraints weight = 45736.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.045212 restraints weight = 29473.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.045786 restraints weight = 22516.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.046048 restraints weight = 19105.904| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16851 Z= 0.101 Angle : 0.543 12.174 22907 Z= 0.278 Chirality : 0.041 0.156 2608 Planarity : 0.003 0.049 2965 Dihedral : 4.527 40.290 2318 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.90 % Allowed : 15.57 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 2142 helix: 1.24 (0.24), residues: 478 sheet: 0.24 (0.22), residues: 531 loop : -1.36 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P1914 TYR 0.014 0.001 TYR P1924 PHE 0.033 0.001 PHE P2119 TRP 0.009 0.001 TRP H 109 HIS 0.004 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00234 (16842) covalent geometry : angle 0.54308 (22889) SS BOND : bond 0.00210 ( 9) SS BOND : angle 0.53439 ( 18) hydrogen bonds : bond 0.03284 ( 481) hydrogen bonds : angle 4.64630 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3790.37 seconds wall clock time: 65 minutes 57.11 seconds (3957.11 seconds total)