Starting phenix.real_space_refine on Mon Dec 11 03:21:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvl_26813/12_2023/7uvl_26813.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvl_26813/12_2023/7uvl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvl_26813/12_2023/7uvl_26813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvl_26813/12_2023/7uvl_26813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvl_26813/12_2023/7uvl_26813.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvl_26813/12_2023/7uvl_26813.pdb" } 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 Residue "P TYR 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 1560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 1604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 1741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 1757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 1823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 1830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 1834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 1929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 2119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 2186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 2193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 9.44, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.09 Conformation dependent library (CDL) restraints added in 3.1 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: 1.93 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: 7.25 Time building geometry restraints manager: 7.51 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: 99.61 - 106.50: 439 106.50 - 113.39: 9348 113.39 - 120.28: 5622 120.28 - 127.17: 7316 127.17 - 134.06: 164 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 2.440 nonbonded pdb=" O VAL P2059 " pdb=" OG SER P2063 " model vdw 2.183 2.440 nonbonded pdb=" O GLU P1330 " pdb=" NZ LYS P1334 " model vdw 2.202 2.520 nonbonded pdb=" OH TYR P1962 " pdb=" OG SER P2031 " model vdw 2.211 2.440 nonbonded pdb=" OD1 ASN P1566 " pdb=" NZ LYS P1575 " model vdw 2.212 2.520 ... (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 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: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 18.100 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 46.920 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.990 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 2.051 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2735 time to fit residues: 32.1336 Evaluate side-chains 49 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.821 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4701 ------------------------------------------------------------------------------- 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: 7.9990 chunk 160 optimal weight: 30.0000 chunk 89 optimal weight: 0.0010 chunk 54 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 overall best weight: 2.5994 ------------------------------------------------------------------------------- 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 ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1927 ASN P2020 ASN ** P2064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS ** H 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8106 moved from start: 0.0996 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= 0.325 Angle : 0.610 6.834 22889 Z= 0.322 Chirality : 0.043 0.168 2608 Planarity : 0.004 0.046 2965 Dihedral : 4.926 41.262 2318 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.50 % Allowed : 7.11 % Favored : 92.38 % 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: -0.76 (0.18), residues: 2142 helix: 0.65 (0.24), residues: 482 sheet: 0.33 (0.23), residues: 501 loop : -1.43 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 36 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 63 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 1.894 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 59 average time/residue: 0.2777 time to fit residues: 27.4884 Evaluate side-chains 57 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 1.809 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1521 time to fit residues: 4.2770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 208 optimal weight: 8.9990 chunk 171 optimal weight: 30.0000 chunk 191 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 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 998 GLN P 999 HIS ** P1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1581 HIS ** P1606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1745 ASN ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P2064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 GLN ** H 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1413 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= 0.329 Angle : 0.596 6.578 22889 Z= 0.315 Chirality : 0.042 0.165 2608 Planarity : 0.004 0.048 2965 Dihedral : 5.025 46.408 2318 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.34 % Allowed : 10.64 % Favored : 88.01 % 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: 0.64 (0.24), residues: 482 sheet: 0.24 (0.23), residues: 503 loop : -1.44 (0.18), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P2134 HIS 0.005 0.001 HIS P1851 PHE 0.035 0.002 PHE P2119 TYR 0.031 0.002 TYR P1348 ARG 0.009 0.001 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 77 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 53 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 73 average time/residue: 0.2741 time to fit residues: 33.3435 Evaluate side-chains 61 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 1.734 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1618 time to fit residues: 6.6279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 5.9990 chunk 145 optimal weight: 0.0670 chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- 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** ** P1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16842 Z= 0.237 Angle : 0.558 8.250 22889 Z= 0.292 Chirality : 0.041 0.163 2608 Planarity : 0.004 0.049 2965 Dihedral : 4.909 45.999 2318 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.18 % Allowed : 13.22 % Favored : 85.60 % 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: 0.75 (0.24), residues: 488 sheet: 0.25 (0.23), residues: 505 loop : -1.41 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 109 HIS 0.005 0.001 HIS P1581 PHE 0.032 0.002 PHE P2119 TYR 0.012 0.001 TYR P1172 ARG 0.005 0.000 ARG L 113 *********************** 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 74 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 53 time to evaluate : 1.919 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 72 average time/residue: 0.2590 time to fit residues: 32.6245 Evaluate side-chains 59 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 1.926 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1597 time to fit residues: 6.1893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 30.0000 chunk 116 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 174 optimal weight: 0.1980 chunk 141 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 104 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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** ** P1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16842 Z= 0.283 Angle : 0.577 11.807 22889 Z= 0.300 Chirality : 0.041 0.195 2608 Planarity : 0.004 0.051 2965 Dihedral : 4.914 46.375 2318 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.40 % Allowed : 14.51 % Favored : 84.09 % 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: -0.76 (0.18), residues: 2142 helix: 0.75 (0.24), residues: 491 sheet: 0.25 (0.23), residues: 505 loop : -1.46 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 109 HIS 0.006 0.001 HIS P1581 PHE 0.031 0.002 PHE P2119 TYR 0.031 0.002 TYR P1348 ARG 0.009 0.000 ARG L 113 *********************** 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 79 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 54 time to evaluate : 2.002 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 74 average time/residue: 0.2716 time to fit residues: 34.1001 Evaluate side-chains 67 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 1.917 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1746 time to fit residues: 7.2702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.3980 chunk 184 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 170 optimal weight: 30.0000 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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** P1892 ASN L 35 HIS ** H 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16842 Z= 0.248 Angle : 0.554 8.857 22889 Z= 0.289 Chirality : 0.041 0.158 2608 Planarity : 0.004 0.051 2965 Dihedral : 4.846 44.926 2318 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.67 % Allowed : 16.02 % Favored : 83.31 % 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: 0.79 (0.24), residues: 491 sheet: 0.23 (0.23), residues: 510 loop : -1.44 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 109 HIS 0.005 0.001 HIS P1581 PHE 0.029 0.002 PHE P2119 TYR 0.014 0.001 TYR P1924 ARG 0.006 0.000 ARG L 113 *********************** 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 69 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 67 average time/residue: 0.2861 time to fit residues: 31.5046 Evaluate side-chains 59 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 1.913 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1857 time to fit residues: 4.3782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** ** P1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P2020 ASN ** H 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16842 Z= 0.321 Angle : 0.599 9.783 22889 Z= 0.311 Chirality : 0.042 0.160 2608 Planarity : 0.004 0.050 2965 Dihedral : 4.938 43.864 2318 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.01 % Allowed : 16.75 % Favored : 82.24 % 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: 0.64 (0.24), residues: 497 sheet: 0.18 (0.23), residues: 495 loop : -1.44 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP H 109 HIS 0.006 0.001 HIS P1581 PHE 0.035 0.002 PHE P2119 TYR 0.033 0.002 TYR P1348 ARG 0.005 0.000 ARG L 113 *********************** 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 69 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 51 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 64 average time/residue: 0.2932 time to fit residues: 31.3178 Evaluate side-chains 63 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 2.115 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2068 time to fit residues: 7.3318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 129 optimal weight: 0.0370 chunk 139 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 185 optimal weight: 20.0000 overall best weight: 2.2066 ------------------------------------------------------------------------------- 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** ** P1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16842 Z= 0.278 Angle : 0.580 10.751 22889 Z= 0.300 Chirality : 0.041 0.157 2608 Planarity : 0.004 0.049 2965 Dihedral : 4.925 43.008 2318 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.45 % Allowed : 16.97 % 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: -0.80 (0.18), residues: 2142 helix: 0.68 (0.24), residues: 497 sheet: 0.15 (0.23), residues: 494 loop : -1.42 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 109 HIS 0.005 0.001 HIS P1581 PHE 0.032 0.002 PHE P2119 TYR 0.014 0.001 TYR P1924 ARG 0.004 0.000 ARG P1774 *********************** 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 61 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 2.142 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 60 average time/residue: 0.2983 time to fit residues: 29.6085 Evaluate side-chains 55 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 2.451 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1809 time to fit residues: 4.1693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 6.9990 chunk 178 optimal weight: 0.0470 chunk 190 optimal weight: 4.9990 chunk 114 optimal weight: 0.0670 chunk 82 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 189 optimal weight: 0.0970 chunk 125 optimal weight: 0.9980 overall best weight: 0.4014 ------------------------------------------------------------------------------- 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** P1672 GLN ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16842 Z= 0.155 Angle : 0.543 11.598 22889 Z= 0.279 Chirality : 0.040 0.168 2608 Planarity : 0.003 0.050 2965 Dihedral : 4.750 42.016 2318 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.34 % Allowed : 17.37 % 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: -0.68 (0.18), residues: 2142 helix: 0.86 (0.24), residues: 495 sheet: 0.16 (0.23), residues: 519 loop : -1.38 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 109 HIS 0.003 0.001 HIS P1847 PHE 0.031 0.001 PHE P2119 TYR 0.020 0.001 TYR P1225 ARG 0.026 0.000 ARG L 113 *********************** 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 64 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 1.975 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.3045 time to fit residues: 30.0064 Evaluate side-chains 56 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 1.985 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1955 time to fit residues: 4.0353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 211 optimal weight: 0.0570 chunk 194 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 133 optimal weight: 0.0010 overall best weight: 1.2108 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16842 Z= 0.193 Angle : 0.551 14.970 22889 Z= 0.280 Chirality : 0.040 0.150 2608 Planarity : 0.003 0.051 2965 Dihedral : 4.677 43.212 2318 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.28 % Allowed : 17.54 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.18), residues: 2142 helix: 0.90 (0.24), residues: 496 sheet: 0.19 (0.23), residues: 519 loop : -1.35 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 109 HIS 0.004 0.001 HIS P1581 PHE 0.030 0.001 PHE P2119 TYR 0.036 0.001 TYR P1348 ARG 0.011 0.000 ARG L 113 ********************** 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 57 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 2.129 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.2727 time to fit residues: 26.1589 Evaluate side-chains 52 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 1.794 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1707 time to fit residues: 3.5193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 155 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** ** P1200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 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 = 0.3783 r_free = 0.3783 target = 0.064935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.040910 restraints weight = 96491.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.042371 restraints weight = 45377.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.043321 restraints weight = 29038.804| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 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 = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16842 Z= 0.332 Angle : 0.626 14.735 22889 Z= 0.318 Chirality : 0.042 0.155 2608 Planarity : 0.004 0.053 2965 Dihedral : 4.910 43.511 2318 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.28 % Allowed : 17.82 % Favored : 81.90 % 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: -0.75 (0.18), residues: 2142 helix: 0.72 (0.24), residues: 497 sheet: 0.17 (0.23), residues: 501 loop : -1.38 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 109 HIS 0.007 0.001 HIS P1581 PHE 0.030 0.002 PHE P2119 TYR 0.015 0.002 TYR P1757 ARG 0.010 0.001 ARG L 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2902.08 seconds wall clock time: 54 minutes 47.98 seconds (3287.98 seconds total)