Starting phenix.real_space_refine on Tue Dec 31 22:11:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uvl_26813/12_2024/7uvl_26813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uvl_26813/12_2024/7uvl_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_26813/12_2024/7uvl_26813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uvl_26813/12_2024/7uvl_26813.map" model { file = "/net/cci-nas-00/data/ceres_data/7uvl_26813/12_2024/7uvl_26813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uvl_26813/12_2024/7uvl_26813.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 6} 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: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 6} 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: 11.01, per 1000 atoms: 0.67 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: 4.17 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.42 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: 8.15 Time building geometry restraints manager: 4.86 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: 5.330 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: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 43.100 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.870 ------------------------------------------------------------------------------- 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 16842 Z= 0.177 Angle : 0.563 8.405 22889 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 : 13.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (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 TRP 0.012 0.001 TRP H 109 HIS 0.005 0.001 HIS P1847 PHE 0.018 0.001 PHE P2193 TYR 0.015 0.001 TYR P1924 ARG 0.005 0.000 ARG L 113 *********************** 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 : 1.986 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: 0.7821 (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: 0.2983 time to fit residues: 35.5275 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 : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 4.9990 chunk 160 optimal weight: 30.0000 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 166 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 192 optimal weight: 20.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1745 ASN ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1927 ASN P2020 ASN L 35 HIS ** H 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16842 Z= 0.382 Angle : 0.646 7.031 22889 Z= 0.342 Chirality : 0.044 0.169 2608 Planarity : 0.004 0.045 2965 Dihedral : 5.016 43.399 2318 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.45 % Allowed : 7.28 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.18), residues: 2142 helix: 0.56 (0.24), residues: 481 sheet: 0.25 (0.23), residues: 512 loop : -1.44 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 160 HIS 0.005 0.001 HIS P1847 PHE 0.041 0.002 PHE P2119 TYR 0.031 0.002 TYR P1348 ARG 0.011 0.001 ARG L 113 *********************** 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 60 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 1.983 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 57 average time/residue: 0.2774 time to fit residues: 27.0309 Evaluate side-chains 53 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 1.905 ------------------------------------------------------------------------------- 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 1985 ILE 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 106 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 160 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 chunk 208 optimal weight: 0.4980 chunk 171 optimal weight: 30.0000 chunk 191 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 154 optimal weight: 0.0170 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** P1322 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16842 Z= 0.159 Angle : 0.534 8.313 22889 Z= 0.282 Chirality : 0.041 0.163 2608 Planarity : 0.004 0.046 2965 Dihedral : 4.779 42.950 2318 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.90 % Allowed : 9.08 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.18), residues: 2142 helix: 0.84 (0.24), residues: 482 sheet: 0.25 (0.22), residues: 513 loop : -1.38 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP P1247 HIS 0.004 0.001 HIS L 35 PHE 0.035 0.001 PHE P2119 TYR 0.028 0.001 TYR P1348 ARG 0.008 0.000 ARG L 113 *********************** 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 74 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 2.051 Fit side-chains revert: symmetry clash REVERT: P 1047 MET cc_start: 0.6503 (tpp) cc_final: 0.6161 (tpp) REVERT: P 1832 MET cc_start: 0.8291 (mmm) cc_final: 0.7824 (mmm) REVERT: P 2019 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8801 (mt) outliers start: 16 outliers final: 5 residues processed: 71 average time/residue: 0.2885 time to fit residues: 33.6994 Evaluate side-chains 56 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 1455 THR Chi-restraints excluded: chain P residue 1778 VAL Chi-restraints excluded: chain P residue 1849 MET Chi-restraints excluded: chain P residue 2000 ILE Chi-restraints excluded: chain P residue 2019 ILE Chi-restraints excluded: chain P residue 2170 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 P1007 ASN P1206 GLN ** P1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16842 Z= 0.382 Angle : 0.642 11.667 22889 Z= 0.335 Chirality : 0.043 0.170 2608 Planarity : 0.004 0.047 2965 Dihedral : 5.021 45.925 2318 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.62 % Allowed : 11.65 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.18), residues: 2142 helix: 0.62 (0.24), residues: 482 sheet: 0.07 (0.22), residues: 529 loop : -1.44 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P1247 HIS 0.005 0.001 HIS P1847 PHE 0.031 0.002 PHE P2119 TYR 0.017 0.002 TYR P1757 ARG 0.005 0.001 ARG P2042 *********************** 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 81 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 52 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 1047 MET cc_start: 0.6806 (tpp) cc_final: 0.6553 (tpp) REVERT: P 2007 ASP cc_start: 0.6319 (t0) cc_final: 0.6080 (t0) outliers start: 29 outliers final: 17 residues processed: 77 average time/residue: 0.2819 time to fit residues: 36.5373 Evaluate side-chains 65 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 2.162 ------------------------------------------------------------------------------- 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 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 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 91 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 174 optimal weight: 0.0770 chunk 141 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 104 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16842 Z= 0.217 Angle : 0.551 8.796 22889 Z= 0.289 Chirality : 0.041 0.179 2608 Planarity : 0.004 0.048 2965 Dihedral : 4.893 44.712 2318 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.46 % Allowed : 13.73 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 2142 helix: 0.78 (0.24), residues: 488 sheet: 0.08 (0.22), residues: 531 loop : -1.38 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P1247 HIS 0.005 0.001 HIS P1581 PHE 0.032 0.002 PHE P2119 TYR 0.031 0.001 TYR P1348 ARG 0.003 0.000 ARG H 50 *********************** 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 77 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 2.317 Fit side-chains revert: symmetry clash REVERT: P 1047 MET cc_start: 0.6835 (tpp) cc_final: 0.6269 (tpp) REVERT: P 2019 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8846 (mt) outliers start: 26 outliers final: 17 residues processed: 73 average time/residue: 0.2644 time to fit residues: 33.1981 Evaluate side-chains 67 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 944 VAL Chi-restraints excluded: chain P residue 1455 THR Chi-restraints excluded: chain P residue 1489 VAL Chi-restraints excluded: chain P residue 1710 ILE 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 1816 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 1943 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 67 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 ** P1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16842 Z= 0.313 Angle : 0.596 8.554 22889 Z= 0.311 Chirality : 0.042 0.164 2608 Planarity : 0.004 0.048 2965 Dihedral : 4.933 43.842 2318 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.96 % Allowed : 14.29 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2142 helix: 0.66 (0.24), residues: 492 sheet: -0.01 (0.22), residues: 534 loop : -1.41 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 109 HIS 0.006 0.001 HIS P1581 PHE 0.030 0.002 PHE P2119 TYR 0.016 0.002 TYR P1757 ARG 0.004 0.000 ARG H 50 *********************** 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 87 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 52 time to evaluate : 2.026 Fit side-chains revert: symmetry clash REVERT: P 1047 MET cc_start: 0.6985 (tpp) cc_final: 0.6357 (tpp) REVERT: L 94 MET cc_start: 0.7111 (ppp) cc_final: 0.6873 (ppp) outliers start: 35 outliers final: 27 residues processed: 82 average time/residue: 0.2656 time to fit residues: 36.9525 Evaluate side-chains 77 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 50 time to evaluate : 2.089 ------------------------------------------------------------------------------- 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 999 HIS Chi-restraints excluded: chain P residue 1010 TYR Chi-restraints excluded: chain P residue 1100 LEU 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 1524 LEU Chi-restraints excluded: chain P residue 1580 TYR Chi-restraints excluded: chain P residue 1710 ILE 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 1816 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 1943 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 197 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 114 optimal weight: 0.2980 chunk 204 optimal weight: 0.8980 chunk 127 optimal weight: 0.0020 chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 P1672 GLN ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16842 Z= 0.155 Angle : 0.533 9.297 22889 Z= 0.278 Chirality : 0.041 0.157 2608 Planarity : 0.003 0.047 2965 Dihedral : 4.723 41.401 2318 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.40 % Allowed : 15.80 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2142 helix: 0.97 (0.24), residues: 486 sheet: 0.12 (0.22), residues: 533 loop : -1.41 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 109 HIS 0.018 0.001 HIS P 999 PHE 0.030 0.001 PHE P2119 TYR 0.034 0.001 TYR P1348 ARG 0.003 0.000 ARG H 50 *********************** 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 79 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 1047 MET cc_start: 0.6997 (tpp) cc_final: 0.6480 (tpp) REVERT: P 1712 MET cc_start: 0.9251 (mtm) cc_final: 0.9046 (mtp) REVERT: P 1832 MET cc_start: 0.8322 (mmm) cc_final: 0.7904 (mmm) REVERT: P 2019 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8818 (mt) REVERT: L 94 MET cc_start: 0.7199 (ppp) cc_final: 0.6957 (ppp) outliers start: 25 outliers final: 19 residues processed: 73 average time/residue: 0.2725 time to fit residues: 33.5610 Evaluate side-chains 72 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 999 HIS Chi-restraints excluded: chain P residue 1100 LEU Chi-restraints excluded: chain P residue 1226 VAL Chi-restraints excluded: chain P residue 1400 VAL Chi-restraints excluded: chain P residue 1455 THR Chi-restraints excluded: chain P residue 1575 LYS Chi-restraints excluded: chain P residue 1580 TYR 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 1816 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 39 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 160 optimal weight: 30.0000 chunk 185 optimal weight: 20.0000 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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 ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 GLN ** H 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16842 Z= 0.326 Angle : 0.598 8.903 22889 Z= 0.311 Chirality : 0.042 0.162 2608 Planarity : 0.004 0.049 2965 Dihedral : 4.854 42.309 2318 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.85 % Allowed : 15.57 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 2142 helix: 0.71 (0.24), residues: 492 sheet: 0.11 (0.22), residues: 518 loop : -1.34 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 109 HIS 0.008 0.001 HIS P1581 PHE 0.035 0.002 PHE P2119 TYR 0.015 0.002 TYR P1757 ARG 0.004 0.000 ARG P2042 *********************** 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 85 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 52 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 29 residues processed: 80 average time/residue: 0.2661 time to fit residues: 35.8587 Evaluate side-chains 80 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 51 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 944 VAL Chi-restraints excluded: chain P residue 999 HIS Chi-restraints excluded: chain P residue 1010 TYR Chi-restraints excluded: chain P residue 1100 LEU Chi-restraints excluded: chain P residue 1226 VAL Chi-restraints excluded: chain P residue 1382 VAL Chi-restraints excluded: chain P residue 1394 LEU Chi-restraints excluded: chain P residue 1455 THR Chi-restraints excluded: chain P residue 1489 VAL Chi-restraints excluded: chain P residue 1524 LEU Chi-restraints excluded: chain P residue 1575 LYS Chi-restraints excluded: chain P residue 1580 TYR Chi-restraints excluded: chain P residue 1710 ILE 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 1816 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 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 P residue 2197 ILE 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 195 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 chunk 190 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 149 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 189 optimal weight: 0.2980 chunk 125 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16842 Z= 0.327 Angle : 0.603 9.278 22889 Z= 0.313 Chirality : 0.042 0.158 2608 Planarity : 0.004 0.048 2965 Dihedral : 4.924 41.099 2318 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.02 % Allowed : 15.69 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 2142 helix: 0.75 (0.24), residues: 485 sheet: 0.08 (0.22), residues: 517 loop : -1.44 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 109 HIS 0.014 0.001 HIS P 999 PHE 0.033 0.002 PHE P2119 TYR 0.035 0.002 TYR P1348 ARG 0.003 0.000 ARG P2042 *********************** 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 89 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 53 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 1047 MET cc_start: 0.5875 (tpp) cc_final: 0.5435 (tpp) REVERT: L 94 MET cc_start: 0.6851 (ppp) cc_final: 0.6649 (ppp) outliers start: 36 outliers final: 29 residues processed: 84 average time/residue: 0.2685 time to fit residues: 37.8703 Evaluate side-chains 81 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 52 time to evaluate : 2.079 ------------------------------------------------------------------------------- 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 1100 LEU Chi-restraints excluded: chain P residue 1226 VAL Chi-restraints excluded: chain P residue 1382 VAL Chi-restraints excluded: chain P residue 1394 LEU 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 1524 LEU Chi-restraints excluded: chain P residue 1575 LYS Chi-restraints excluded: chain P residue 1580 TYR Chi-restraints excluded: chain P residue 1710 ILE 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 1943 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 95 optimal weight: 0.3980 chunk 139 optimal weight: 0.0010 chunk 211 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 133 optimal weight: 0.3980 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16842 Z= 0.180 Angle : 0.548 10.070 22889 Z= 0.283 Chirality : 0.041 0.158 2608 Planarity : 0.003 0.049 2965 Dihedral : 4.737 39.683 2318 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.57 % Allowed : 16.30 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.18), residues: 2142 helix: 0.99 (0.24), residues: 486 sheet: 0.10 (0.22), residues: 532 loop : -1.40 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 109 HIS 0.003 0.001 HIS P1847 PHE 0.033 0.001 PHE P2119 TYR 0.013 0.001 TYR P1732 ARG 0.002 0.000 ARG P1914 ********************** 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 82 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 54 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 1047 MET cc_start: 0.5891 (tpp) cc_final: 0.5419 (tpp) REVERT: P 2019 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8820 (mt) REVERT: L 94 MET cc_start: 0.6974 (ppp) cc_final: 0.6700 (ppp) outliers start: 28 outliers final: 23 residues processed: 77 average time/residue: 0.3224 time to fit residues: 41.2137 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 : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 944 VAL Chi-restraints excluded: chain P residue 999 HIS Chi-restraints excluded: chain P residue 1010 TYR Chi-restraints excluded: chain P residue 1100 LEU Chi-restraints excluded: chain P residue 1226 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 1575 LYS Chi-restraints excluded: chain P residue 1580 TYR 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 1943 VAL 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 4 MET 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 179 optimal weight: 30.0000 chunk 51 optimal weight: 6.9990 chunk 155 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 172 optimal weight: 0.0030 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.065280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.042197 restraints weight = 97116.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.043762 restraints weight = 51625.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.043864 restraints weight = 28648.671| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16842 Z= 0.283 Angle : 0.586 9.636 22889 Z= 0.303 Chirality : 0.042 0.151 2608 Planarity : 0.004 0.048 2965 Dihedral : 4.795 41.650 2318 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.40 % Allowed : 16.64 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2142 helix: 0.91 (0.24), residues: 486 sheet: 0.11 (0.23), residues: 518 loop : -1.36 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP H 109 HIS 0.020 0.001 HIS P 999 PHE 0.032 0.002 PHE P2119 TYR 0.035 0.002 TYR P1348 ARG 0.002 0.000 ARG P2042 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2866.95 seconds wall clock time: 54 minutes 30.64 seconds (3270.64 seconds total)