Starting phenix.real_space_refine on Tue Apr 9 23:20:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v86_21096/04_2024/6v86_21096.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v86_21096/04_2024/6v86_21096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v86_21096/04_2024/6v86_21096.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v86_21096/04_2024/6v86_21096.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v86_21096/04_2024/6v86_21096.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v86_21096/04_2024/6v86_21096.pdb" } resolution = 4.63 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 97 5.16 5 C 11364 2.51 5 N 3027 2.21 5 O 3291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 311": "NH1" <-> "NH2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "A ARG 782": "NH1" <-> "NH2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 835": "NH1" <-> "NH2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A ARG 929": "NH1" <-> "NH2" Residue "A ARG 984": "NH1" <-> "NH2" Residue "A ARG 1047": "NH1" <-> "NH2" Residue "A ARG 1052": "NH1" <-> "NH2" Residue "A ARG 1058": "NH1" <-> "NH2" Residue "A ARG 1083": "NH1" <-> "NH2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A GLU 1091": "OE1" <-> "OE2" Residue "A ARG 1098": "NH1" <-> "NH2" Residue "A ARG 1156": "NH1" <-> "NH2" Residue "A ARG 1207": "NH1" <-> "NH2" Residue "A GLU 1258": "OE1" <-> "OE2" Residue "A ARG 1446": "NH1" <-> "NH2" Residue "A GLU 1486": "OE1" <-> "OE2" Residue "A GLU 1741": "OE1" <-> "OE2" Residue "A ARG 1792": "NH1" <-> "NH2" Residue "A GLU 1819": "OE1" <-> "OE2" Residue "A PHE 1956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1968": "OE1" <-> "OE2" Residue "A ARG 1969": "NH1" <-> "NH2" Residue "A GLU 2039": "OE1" <-> "OE2" Residue "A GLU 2083": "OE1" <-> "OE2" Residue "A ARG 2175": "NH1" <-> "NH2" Residue "C GLU 221": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17781 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 15103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1890, 15103 Classifications: {'peptide': 1890} Link IDs: {'PTRANS': 84, 'TRANS': 1805} Chain breaks: 28 Chain: "B" Number of atoms: 569 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 72, 545 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Conformer: "B" Number of residues, atoms: 72, 545 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} bond proxies already assigned to first conformer: 517 Chain: "C" Number of atoms: 582 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 74, 559 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Conformer: "B" Number of residues, atoms: 74, 559 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} bond proxies already assigned to first conformer: 532 Chain: "D" Number of atoms: 569 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 72, 545 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Conformer: "B" Number of residues, atoms: 72, 545 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} bond proxies already assigned to first conformer: 517 Chain: "E" Number of atoms: 582 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 74, 559 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Conformer: "B" Number of residues, atoms: 74, 559 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} bond proxies already assigned to first conformer: 532 Chain: "F" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 374 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9936 SG CYS A1373 115.412 56.251 104.943 1.00123.58 S ATOM 9942 SG CYS A1374 112.735 58.424 105.844 1.00114.32 S ATOM 8621 SG CYS A1184 109.520 46.468 88.283 1.00 30.00 S Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N ASER B 211 " occ=0.48 ... (10 atoms not shown) pdb=" OG BSER B 211 " occ=0.52 residue: pdb=" N GLU B 221 " occ=0.84 ... (7 atoms not shown) pdb=" OE2 GLU B 221 " occ=0.84 residue: pdb=" N AASN B 228 " occ=0.42 ... (14 atoms not shown) pdb=" ND2BASN B 228 " occ=0.58 residue: pdb=" N AASN C 220 " occ=0.37 ... (14 atoms not shown) pdb=" ND2BASN C 220 " occ=0.63 residue: pdb=" N ASER C 231 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER C 231 " occ=0.40 residue: pdb=" N ASER D 211 " occ=0.48 ... (10 atoms not shown) pdb=" OG BSER D 211 " occ=0.52 residue: pdb=" N GLU D 221 " occ=0.84 ... (7 atoms not shown) pdb=" OE2 GLU D 221 " occ=0.84 residue: pdb=" N AASN D 228 " occ=0.42 ... (14 atoms not shown) pdb=" ND2BASN D 228 " occ=0.58 residue: pdb=" N AASN E 220 " occ=0.37 ... (14 atoms not shown) pdb=" ND2BASN E 220 " occ=0.63 residue: pdb=" N ASER E 231 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER E 231 " occ=0.40 Time building chain proxies: 10.27, per 1000 atoms: 0.58 Number of scatterers: 17781 At special positions: 0 Unit cell: (184.8, 144.48, 138.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 97 16.00 O 3291 8.00 N 3027 7.00 C 11364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.40 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1374 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1373 " pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1184 " pdb="ZN ZN A2302 " - pdb=" NE2 HIS A1368 " pdb="ZN ZN A2302 " - pdb=" ND1 HIS A1366 " 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4274 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 7 sheets defined 61.6% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 49 through 55 Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 93 through 98 Processing helix chain 'A' and resid 107 through 140 removed outlier: 3.758A pdb=" N LYS A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLY A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 170 Processing helix chain 'A' and resid 173 through 197 Processing helix chain 'A' and resid 235 through 257 removed outlier: 3.935A pdb=" N VAL A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 261 through 282 removed outlier: 3.787A pdb=" N LYS A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 302 removed outlier: 4.311A pdb=" N TYR A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 328 removed outlier: 4.174A pdb=" N ALA A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 346 Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.612A pdb=" N THR A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 removed outlier: 4.185A pdb=" N ALA A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 413 Processing helix chain 'A' and resid 427 through 436 Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.775A pdb=" N LYS A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 513 through 520 removed outlier: 3.529A pdb=" N ASN A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 566 through 584 Processing helix chain 'A' and resid 597 through 611 Processing helix chain 'A' and resid 672 through 675 Processing helix chain 'A' and resid 676 through 687 Processing helix chain 'A' and resid 694 through 700 Processing helix chain 'A' and resid 743 through 762 removed outlier: 3.514A pdb=" N TRP A 747 " --> pdb=" O CYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 815 removed outlier: 3.754A pdb=" N LYS A 792 " --> pdb=" O PRO A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 821 No H-bonds generated for 'chain 'A' and resid 819 through 821' Processing helix chain 'A' and resid 846 through 852 Processing helix chain 'A' and resid 863 through 881 removed outlier: 3.663A pdb=" N SER A 867 " --> pdb=" O CYS A 863 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN A 881 " --> pdb=" O ARG A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 905 removed outlier: 3.625A pdb=" N CYS A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 922 Processing helix chain 'A' and resid 923 through 932 removed outlier: 4.380A pdb=" N VAL A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 938 Processing helix chain 'A' and resid 945 through 950 Processing helix chain 'A' and resid 955 through 971 removed outlier: 3.727A pdb=" N SER A 959 " --> pdb=" O ASP A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 983 removed outlier: 4.457A pdb=" N TYR A 979 " --> pdb=" O TYR A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 996 Processing helix chain 'A' and resid 1008 through 1024 removed outlier: 3.695A pdb=" N ALA A1012 " --> pdb=" O PRO A1008 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1032 removed outlier: 3.744A pdb=" N GLY A1032 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1051 removed outlier: 3.510A pdb=" N ASP A1051 " --> pdb=" O ARG A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1067 removed outlier: 3.800A pdb=" N ALA A1060 " --> pdb=" O PHE A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1078 removed outlier: 3.608A pdb=" N ARG A1071 " --> pdb=" O THR A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1091 Processing helix chain 'A' and resid 1097 through 1105 removed outlier: 3.954A pdb=" N ASP A1105 " --> pdb=" O ASN A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1117 removed outlier: 3.612A pdb=" N ASN A1109 " --> pdb=" O ASP A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1132 Processing helix chain 'A' and resid 1136 through 1154 Proline residue: A1151 - end of helix Processing helix chain 'A' and resid 1165 through 1170 Processing helix chain 'A' and resid 1238 through 1251 removed outlier: 3.985A pdb=" N TRP A1251 " --> pdb=" O GLY A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1271 removed outlier: 3.543A pdb=" N TRP A1260 " --> pdb=" O THR A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1352 Processing helix chain 'A' and resid 1437 through 1453 removed outlier: 4.116A pdb=" N SER A1441 " --> pdb=" O LEU A1437 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A1451 " --> pdb=" O GLN A1447 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A1452 " --> pdb=" O ILE A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1504 removed outlier: 3.872A pdb=" N TYR A1504 " --> pdb=" O SER A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1523 Processing helix chain 'A' and resid 1525 through 1537 removed outlier: 4.054A pdb=" N ALA A1529 " --> pdb=" O ILE A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1549 removed outlier: 4.172A pdb=" N ARG A1544 " --> pdb=" O PRO A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1586 Processing helix chain 'A' and resid 1605 through 1624 Processing helix chain 'A' and resid 1636 through 1650 Processing helix chain 'A' and resid 1656 through 1663 removed outlier: 4.241A pdb=" N LEU A1660 " --> pdb=" O SER A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1688 Processing helix chain 'A' and resid 1695 through 1701 removed outlier: 3.654A pdb=" N ALA A1699 " --> pdb=" O GLY A1696 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A1700 " --> pdb=" O GLN A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1775 removed outlier: 4.176A pdb=" N HIS A1771 " --> pdb=" O ALA A1768 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A1772 " --> pdb=" O PRO A1769 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A1775 " --> pdb=" O HIS A1772 " (cutoff:3.500A) Processing helix chain 'A' and resid 1784 through 1796 Processing helix chain 'A' and resid 1815 through 1822 removed outlier: 3.709A pdb=" N GLU A1819 " --> pdb=" O MET A1815 " (cutoff:3.500A) Processing helix chain 'A' and resid 1849 through 1855 Processing helix chain 'A' and resid 1855 through 1861 Processing helix chain 'A' and resid 1891 through 1899 Processing helix chain 'A' and resid 1923 through 1935 Processing helix chain 'A' and resid 1952 through 1964 Processing helix chain 'A' and resid 2001 through 2012 removed outlier: 3.626A pdb=" N GLY A2005 " --> pdb=" O SER A2001 " (cutoff:3.500A) Processing helix chain 'A' and resid 2021 through 2046 removed outlier: 4.359A pdb=" N GLN A2025 " --> pdb=" O GLU A2021 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A2046 " --> pdb=" O ASP A2042 " (cutoff:3.500A) Processing helix chain 'A' and resid 2053 through 2059 Processing helix chain 'A' and resid 2083 through 2104 Processing helix chain 'A' and resid 2126 through 2144 Processing helix chain 'A' and resid 2149 through 2161 Processing helix chain 'A' and resid 2171 through 2175 removed outlier: 3.642A pdb=" N ARG A2175 " --> pdb=" O ASN A2172 " (cutoff:3.500A) Processing helix chain 'A' and resid 2187 through 2191 Processing helix chain 'A' and resid 2194 through 2200 Processing helix chain 'A' and resid 2208 through 2226 removed outlier: 3.668A pdb=" N HIS A2226 " --> pdb=" O VAL A2222 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 247 Processing helix chain 'B' and resid 248 through 269 Processing helix chain 'C' and resid 202 through 269 Processing helix chain 'D' and resid 204 through 247 removed outlier: 4.340A pdb=" N LEU D 208 " --> pdb=" O ASP D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 270 removed outlier: 4.128A pdb=" N MET D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 270 removed outlier: 4.107A pdb=" N LEU E 205 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER E 248 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N MET E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 356 Processing helix chain 'F' and resid 360 through 374 removed outlier: 3.656A pdb=" N GLN F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 390 Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 208 removed outlier: 3.928A pdb=" N ASN A 208 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 211 " --> pdb=" O ASN A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 222 Processing sheet with id=AA3, first strand: chain 'A' and resid 765 through 771 Processing sheet with id=AA4, first strand: chain 'A' and resid 704 through 705 Processing sheet with id=AA5, first strand: chain 'A' and resid 829 through 832 Processing sheet with id=AA6, first strand: chain 'A' and resid 1173 through 1176 removed outlier: 4.160A pdb=" N THR A1192 " --> pdb=" O LEU A1367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1828 through 1829 removed outlier: 7.058A pdb=" N LEU A1805 " --> pdb=" O HIS A1909 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ASP A1911 " --> pdb=" O LEU A1805 " (cutoff:3.500A) 1016 hydrogen bonds defined for protein. 2977 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: 7.00 Time building geometry restraints manager: 7.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5702 1.34 - 1.46: 2644 1.46 - 1.58: 9609 1.58 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 18109 Sorted by residual: bond pdb=" N ILE A1737 " pdb=" CA ILE A1737 " ideal model delta sigma weight residual 1.460 1.493 -0.033 8.60e-03 1.35e+04 1.49e+01 bond pdb=" N ILE A1740 " pdb=" CA ILE A1740 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.11e-02 8.12e+03 1.28e+01 bond pdb=" N ILE A1739 " pdb=" CA ILE A1739 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" N ILE A1970 " pdb=" CA ILE A1970 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.22e-02 6.72e+03 8.87e+00 bond pdb=" N PHE A1967 " pdb=" CA PHE A1967 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.23e-02 6.61e+03 8.54e+00 ... (remaining 18104 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.53: 474 106.53 - 113.47: 10317 113.47 - 120.42: 6882 120.42 - 127.37: 6716 127.37 - 134.31: 172 Bond angle restraints: 24561 Sorted by residual: angle pdb=" N ILE A1737 " pdb=" CA ILE A1737 " pdb=" C ILE A1737 " ideal model delta sigma weight residual 113.71 108.17 5.54 9.50e-01 1.11e+00 3.40e+01 angle pdb=" C ILE A1736 " pdb=" N ILE A1737 " pdb=" CA ILE A1737 " ideal model delta sigma weight residual 121.53 128.87 -7.34 1.40e+00 5.10e-01 2.75e+01 angle pdb=" C SER A 304 " pdb=" N ASP A 305 " pdb=" CA ASP A 305 " ideal model delta sigma weight residual 120.58 127.24 -6.66 1.32e+00 5.74e-01 2.54e+01 angle pdb=" N VAL A 12 " pdb=" CA VAL A 12 " pdb=" C VAL A 12 " ideal model delta sigma weight residual 113.20 108.48 4.72 9.60e-01 1.09e+00 2.41e+01 angle pdb=" CA ILE A1736 " pdb=" C ILE A1736 " pdb=" N ILE A1737 " ideal model delta sigma weight residual 116.60 109.89 6.71 1.45e+00 4.76e-01 2.14e+01 ... (remaining 24556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 9795 17.88 - 35.76: 1020 35.76 - 53.64: 131 53.64 - 71.52: 41 71.52 - 89.40: 14 Dihedral angle restraints: 11001 sinusoidal: 4427 harmonic: 6574 Sorted by residual: dihedral pdb=" CA ASN A1763 " pdb=" C ASN A1763 " pdb=" N PHE A1764 " pdb=" CA PHE A1764 " ideal model delta harmonic sigma weight residual 180.00 151.09 28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA PRO A 714 " pdb=" C PRO A 714 " pdb=" N ALA A 715 " pdb=" CA ALA A 715 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA VAL A1855 " pdb=" C VAL A1855 " pdb=" N PRO A1856 " pdb=" CA PRO A1856 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 10998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2328 0.053 - 0.106: 479 0.106 - 0.159: 76 0.159 - 0.213: 12 0.213 - 0.266: 3 Chirality restraints: 2898 Sorted by residual: chirality pdb=" CB ILE A1740 " pdb=" CA ILE A1740 " pdb=" CG1 ILE A1740 " pdb=" CG2 ILE A1740 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ILE A1970 " pdb=" N ILE A1970 " pdb=" C ILE A1970 " pdb=" CB ILE A1970 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA LEU A1746 " pdb=" N LEU A1746 " pdb=" C LEU A1746 " pdb=" CB LEU A1746 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2895 not shown) Planarity restraints: 3087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A1736 " -0.028 2.00e-02 2.50e+03 5.92e-02 3.51e+01 pdb=" C ILE A1736 " 0.102 2.00e-02 2.50e+03 pdb=" O ILE A1736 " -0.041 2.00e-02 2.50e+03 pdb=" N ILE A1737 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A1738 " 0.021 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C TRP A1738 " -0.077 2.00e-02 2.50e+03 pdb=" O TRP A1738 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE A1739 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1925 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.98e+00 pdb=" N PRO A1926 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A1926 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1926 " -0.037 5.00e-02 4.00e+02 ... (remaining 3084 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 17 2.16 - 2.84: 6151 2.84 - 3.53: 28068 3.53 - 4.21: 39656 4.21 - 4.90: 65684 Nonbonded interactions: 139576 Sorted by model distance: nonbonded pdb=" O ILE A1739 " pdb=" NH2 ARG A2022 " model vdw 1.470 2.520 nonbonded pdb=" O LEU A1746 " pdb=" NZ LYS A1748 " model vdw 1.484 2.520 nonbonded pdb=" O ILE A1739 " pdb=" NH1 ARG A2022 " model vdw 1.668 2.520 nonbonded pdb=" O ILE A1739 " pdb=" CZ ARG A2022 " model vdw 1.735 3.270 nonbonded pdb=" O ALA A1744 " pdb=" NE1 TRP A1964 " model vdw 1.889 2.520 ... (remaining 139571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 199 through 210 or resid 212 through 216 or resid 218 thro \ ugh 219 or resid 221 through 227 or resid 229 through 230 or resid 232 through 2 \ 34 or resid 236 through 270)) selection = (chain 'C' and (resid 199 through 210 or resid 212 through 216 or resid 218 thro \ ugh 219 or resid 221 through 227 or resid 229 through 230 or resid 232 through 2 \ 34 or resid 236 through 270)) selection = (chain 'D' and (resid 199 through 210 or resid 212 through 216 or resid 218 thro \ ugh 219 or resid 221 through 227 or resid 229 through 230 or resid 232 through 2 \ 34 or resid 236 through 270)) selection = (chain 'E' and (resid 199 through 210 or resid 212 through 216 or resid 218 thro \ ugh 219 or resid 221 through 227 or resid 229 through 230 or resid 232 through 2 \ 34 or resid 236 through 270)) } 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=0.00 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: 2.700 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: 10.320 Check model and map are aligned: 0.260 Set scattering table: 0.190 Process input model: 54.680 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.100 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18109 Z= 0.251 Angle : 0.832 10.119 24561 Z= 0.490 Chirality : 0.045 0.266 2898 Planarity : 0.005 0.066 3087 Dihedral : 14.791 89.398 6727 Min Nonbonded Distance : 1.470 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.14 % Favored : 86.63 % Rotamer: Outliers : 0.70 % Allowed : 7.11 % Favored : 92.19 % 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: -4.51 (0.14), residues: 2193 helix: -1.80 (0.12), residues: 1287 sheet: -3.13 (0.53), residues: 69 loop : -4.95 (0.15), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A1950 HIS 0.006 0.001 HIS A1392 PHE 0.018 0.002 PHE A 562 TYR 0.020 0.002 TYR A 85 ARG 0.007 0.001 ARG A1974 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 281 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.9207 (mt) cc_final: 0.8731 (tt) REVERT: A 365 LEU cc_start: 0.8021 (pt) cc_final: 0.7804 (pt) REVERT: A 384 MET cc_start: 0.6840 (tpp) cc_final: 0.6135 (tpt) REVERT: A 435 MET cc_start: 0.8807 (mmm) cc_final: 0.8403 (tmm) REVERT: A 569 MET cc_start: 0.8020 (tpt) cc_final: 0.7727 (tpt) REVERT: A 577 GLU cc_start: 0.7246 (tp30) cc_final: 0.7045 (tp30) REVERT: A 1129 LYS cc_start: 0.9210 (tmmt) cc_final: 0.8811 (mttm) REVERT: A 1447 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8172 (mm-40) REVERT: A 1489 MET cc_start: 0.8181 (ttp) cc_final: 0.7902 (ttp) REVERT: A 1761 PHE cc_start: 0.7982 (t80) cc_final: 0.7538 (t80) REVERT: A 1815 MET cc_start: 0.9101 (pmm) cc_final: 0.8872 (pmm) REVERT: A 1920 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 1923 LEU cc_start: 0.8780 (pt) cc_final: 0.8294 (pp) REVERT: B 233 MET cc_start: 0.8091 (mtt) cc_final: 0.7866 (mtt) REVERT: B 237 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8799 (mt-10) REVERT: C 270 MET cc_start: 0.8669 (mtm) cc_final: 0.7943 (pmm) REVERT: F 348 ILE cc_start: 0.8782 (mm) cc_final: 0.8554 (mp) outliers start: 7 outliers final: 0 residues processed: 285 average time/residue: 0.3126 time to fit residues: 136.4771 Evaluate side-chains 183 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 0.4980 chunk 128 optimal weight: 0.0170 chunk 200 optimal weight: 0.9980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS A 368 HIS A 609 GLN A 670 GLN A 771 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN A 892 ASN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 HIS ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN A1107 ASN ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1289 ASN A1327 ASN A1338 GLN A1352 ASN A1447 GLN ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1679 ASN A1733 ASN ** A1771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1929 ASN A2030 HIS B 202 GLN B 206 ASN B 220 ASN A ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 GLN D 202 GLN D 228 ASN A ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN B E 235 GLN B E 255 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18109 Z= 0.196 Angle : 0.709 10.232 24561 Z= 0.360 Chirality : 0.042 0.309 2898 Planarity : 0.005 0.060 3087 Dihedral : 6.070 69.643 2409 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.97 % Favored : 88.94 % Rotamer: Outliers : 0.65 % Allowed : 6.52 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.17), residues: 2193 helix: -0.10 (0.14), residues: 1322 sheet: -2.76 (0.53), residues: 74 loop : -4.61 (0.16), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A1738 HIS 0.005 0.001 HIS A 816 PHE 0.017 0.001 PHE A2052 TYR 0.021 0.001 TYR A1113 ARG 0.003 0.000 ARG A1244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 276 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 GLU cc_start: 0.8512 (mp0) cc_final: 0.8280 (mp0) REVERT: A 240 MET cc_start: 0.8179 (ttp) cc_final: 0.7058 (ttt) REVERT: A 244 MET cc_start: 0.8444 (mtp) cc_final: 0.7824 (mtp) REVERT: A 370 MET cc_start: 0.7061 (ptm) cc_final: 0.6773 (ptm) REVERT: A 384 MET cc_start: 0.6621 (tpp) cc_final: 0.6135 (tpt) REVERT: A 435 MET cc_start: 0.8774 (mmm) cc_final: 0.8305 (tmm) REVERT: A 569 MET cc_start: 0.8042 (tpt) cc_final: 0.7746 (tpt) REVERT: A 771 GLN cc_start: 0.6250 (OUTLIER) cc_final: 0.6011 (mm-40) REVERT: A 812 PHE cc_start: 0.8939 (t80) cc_final: 0.8663 (t80) REVERT: A 1022 MET cc_start: 0.8546 (mmt) cc_final: 0.8098 (mmm) REVERT: A 1033 ILE cc_start: 0.8132 (mp) cc_final: 0.7858 (mm) REVERT: A 1129 LYS cc_start: 0.9072 (tmmt) cc_final: 0.8553 (mttp) REVERT: A 1133 LEU cc_start: 0.8171 (tp) cc_final: 0.7866 (pp) REVERT: A 1341 MET cc_start: 0.8408 (mmt) cc_final: 0.8110 (mmt) REVERT: A 1447 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8102 (mm-40) REVERT: A 1815 MET cc_start: 0.9021 (pmm) cc_final: 0.8376 (pmm) REVERT: A 1923 LEU cc_start: 0.8784 (pt) cc_final: 0.8253 (pp) REVERT: A 1973 LEU cc_start: 0.8149 (tt) cc_final: 0.7472 (mp) REVERT: A 2162 PHE cc_start: 0.7924 (m-80) cc_final: 0.7287 (m-80) REVERT: B 237 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8738 (mt-10) REVERT: B 258 VAL cc_start: 0.8650 (t) cc_final: 0.8442 (m) REVERT: C 242 ARG cc_start: 0.8924 (tpp80) cc_final: 0.8650 (tpt170) REVERT: C 264 MET cc_start: 0.8594 (ppp) cc_final: 0.8340 (ppp) REVERT: C 270 MET cc_start: 0.8642 (mtm) cc_final: 0.8188 (pmm) REVERT: F 350 LEU cc_start: 0.8723 (mt) cc_final: 0.8500 (tt) outliers start: 6 outliers final: 0 residues processed: 278 average time/residue: 0.3164 time to fit residues: 134.4875 Evaluate side-chains 190 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 201 optimal weight: 0.9980 chunk 217 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 161 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1319 ASN A1338 GLN ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18109 Z= 0.226 Angle : 0.706 11.720 24561 Z= 0.360 Chirality : 0.042 0.169 2898 Planarity : 0.005 0.055 3087 Dihedral : 6.024 69.639 2409 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.22 % Favored : 87.69 % Rotamer: Outliers : 0.40 % Allowed : 6.97 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.18), residues: 2193 helix: 0.34 (0.14), residues: 1325 sheet: -2.74 (0.53), residues: 76 loop : -4.45 (0.17), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1738 HIS 0.006 0.001 HIS A1392 PHE 0.022 0.002 PHE A2052 TYR 0.018 0.002 TYR A2194 ARG 0.004 0.000 ARG A2153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8157 (ttp) cc_final: 0.7158 (ttt) REVERT: A 244 MET cc_start: 0.8273 (mtp) cc_final: 0.7781 (mtp) REVERT: A 384 MET cc_start: 0.6545 (tpp) cc_final: 0.6019 (tpt) REVERT: A 435 MET cc_start: 0.8731 (mmm) cc_final: 0.8331 (tmm) REVERT: A 569 MET cc_start: 0.7913 (tpt) cc_final: 0.7627 (tpt) REVERT: A 812 PHE cc_start: 0.8937 (t80) cc_final: 0.8659 (t80) REVERT: A 1022 MET cc_start: 0.8464 (mmt) cc_final: 0.8179 (mmm) REVERT: A 1489 MET cc_start: 0.8181 (ttp) cc_final: 0.7964 (ttp) REVERT: A 1520 MET cc_start: 0.7968 (tpp) cc_final: 0.7693 (tpp) REVERT: A 1613 LYS cc_start: 0.9120 (tttp) cc_final: 0.8906 (tppt) REVERT: A 1815 MET cc_start: 0.9055 (pmm) cc_final: 0.8366 (pmm) REVERT: A 1920 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7729 (tm-30) REVERT: A 1923 LEU cc_start: 0.8555 (pt) cc_final: 0.8112 (pp) REVERT: A 1973 LEU cc_start: 0.8204 (tt) cc_final: 0.7575 (mp) REVERT: A 2162 PHE cc_start: 0.7804 (m-80) cc_final: 0.7281 (m-80) REVERT: B 233 MET cc_start: 0.7800 (mtm) cc_final: 0.7205 (ppp) REVERT: B 237 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8362 (mt-10) REVERT: B 258 VAL cc_start: 0.8698 (t) cc_final: 0.8479 (m) REVERT: C 242 ARG cc_start: 0.9029 (tpp80) cc_final: 0.8719 (tpt170) REVERT: C 270 MET cc_start: 0.8711 (mtm) cc_final: 0.8005 (pmm) REVERT: D 264 MET cc_start: 0.8305 (tmm) cc_final: 0.8072 (tpt) REVERT: F 350 LEU cc_start: 0.8775 (mt) cc_final: 0.8468 (tt) outliers start: 1 outliers final: 1 residues processed: 249 average time/residue: 0.3043 time to fit residues: 117.1165 Evaluate side-chains 186 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 213 optimal weight: 0.9980 chunk 105 optimal weight: 0.0670 chunk 191 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1771 HIS ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18109 Z= 0.223 Angle : 0.709 9.572 24561 Z= 0.361 Chirality : 0.042 0.220 2898 Planarity : 0.005 0.055 3087 Dihedral : 5.991 69.802 2409 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.40 % Favored : 87.60 % Rotamer: Outliers : 0.35 % Allowed : 5.67 % Favored : 93.98 % 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: -1.83 (0.18), residues: 2193 helix: 0.55 (0.14), residues: 1328 sheet: -2.63 (0.55), residues: 73 loop : -4.35 (0.17), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 113 HIS 0.005 0.001 HIS A1392 PHE 0.019 0.002 PHE A2052 TYR 0.020 0.002 TYR F 367 ARG 0.007 0.000 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7877 (ttp) cc_final: 0.7544 (ttt) REVERT: A 240 MET cc_start: 0.8132 (ttp) cc_final: 0.7185 (ttt) REVERT: A 244 MET cc_start: 0.8322 (mtp) cc_final: 0.7853 (mtp) REVERT: A 384 MET cc_start: 0.6481 (tpp) cc_final: 0.6001 (tpt) REVERT: A 435 MET cc_start: 0.8713 (mmm) cc_final: 0.8330 (tmm) REVERT: A 569 MET cc_start: 0.7873 (tpt) cc_final: 0.7495 (tpt) REVERT: A 812 PHE cc_start: 0.8946 (t80) cc_final: 0.8702 (t80) REVERT: A 1447 GLN cc_start: 0.8544 (mm-40) cc_final: 0.7963 (tm-30) REVERT: A 1520 MET cc_start: 0.8067 (tpp) cc_final: 0.7786 (tpp) REVERT: A 1923 LEU cc_start: 0.8661 (pt) cc_final: 0.8129 (pp) REVERT: A 1973 LEU cc_start: 0.8269 (tt) cc_final: 0.7681 (mp) REVERT: A 2162 PHE cc_start: 0.7676 (m-80) cc_final: 0.7182 (m-80) REVERT: B 237 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8506 (mt-10) REVERT: B 258 VAL cc_start: 0.8698 (t) cc_final: 0.8471 (m) REVERT: C 236 LEU cc_start: 0.8019 (mt) cc_final: 0.7201 (mt) REVERT: C 242 ARG cc_start: 0.9008 (tpp80) cc_final: 0.8731 (tpt170) REVERT: C 270 MET cc_start: 0.8613 (mtm) cc_final: 0.8047 (pmm) REVERT: F 350 LEU cc_start: 0.8755 (mt) cc_final: 0.8408 (tt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.3050 time to fit residues: 115.7632 Evaluate side-chains 177 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 191 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN A 582 ASN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN A1447 GLN ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN A ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18109 Z= 0.207 Angle : 0.712 16.645 24561 Z= 0.354 Chirality : 0.042 0.197 2898 Planarity : 0.005 0.052 3087 Dihedral : 5.873 69.897 2409 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.31 % Favored : 87.69 % Rotamer: Outliers : 0.35 % Allowed : 4.58 % Favored : 95.07 % 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: -1.59 (0.18), residues: 2193 helix: 0.73 (0.14), residues: 1326 sheet: -2.52 (0.56), residues: 71 loop : -4.24 (0.18), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 113 HIS 0.005 0.001 HIS A1539 PHE 0.020 0.002 PHE A2052 TYR 0.021 0.002 TYR A1337 ARG 0.006 0.000 ARG A1775 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.7838 (ttp) cc_final: 0.6890 (ttt) REVERT: A 244 MET cc_start: 0.8315 (mtp) cc_final: 0.7906 (mtp) REVERT: A 384 MET cc_start: 0.6461 (tpp) cc_final: 0.6070 (tpt) REVERT: A 435 MET cc_start: 0.8690 (mmm) cc_final: 0.8310 (tmm) REVERT: A 569 MET cc_start: 0.7824 (tpt) cc_final: 0.7452 (tpt) REVERT: A 812 PHE cc_start: 0.8865 (t80) cc_final: 0.8639 (t80) REVERT: A 1447 GLN cc_start: 0.8607 (mm110) cc_final: 0.8152 (tm-30) REVERT: A 1520 MET cc_start: 0.8148 (tpp) cc_final: 0.7892 (tpp) REVERT: A 1815 MET cc_start: 0.9053 (pmm) cc_final: 0.8365 (pmm) REVERT: A 1973 LEU cc_start: 0.8283 (tt) cc_final: 0.7655 (mp) REVERT: A 2162 PHE cc_start: 0.7211 (m-80) cc_final: 0.6966 (m-80) REVERT: B 237 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8584 (mt-10) REVERT: B 258 VAL cc_start: 0.8716 (t) cc_final: 0.8494 (m) REVERT: C 236 LEU cc_start: 0.7745 (mt) cc_final: 0.7431 (mt) REVERT: C 242 ARG cc_start: 0.9047 (tpp80) cc_final: 0.8697 (tpt170) REVERT: C 270 MET cc_start: 0.8621 (mtm) cc_final: 0.8008 (pmm) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.3132 time to fit residues: 119.9536 Evaluate side-chains 182 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 0.2980 chunk 192 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 213 optimal weight: 0.9990 chunk 177 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN A1319 ASN ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18109 Z= 0.195 Angle : 0.699 13.957 24561 Z= 0.346 Chirality : 0.042 0.211 2898 Planarity : 0.005 0.050 3087 Dihedral : 5.710 69.554 2409 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 0.35 % Allowed : 2.19 % Favored : 97.46 % 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: -1.38 (0.18), residues: 2193 helix: 0.90 (0.14), residues: 1326 sheet: -2.47 (0.55), residues: 75 loop : -4.16 (0.18), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 113 HIS 0.004 0.001 HIS A1539 PHE 0.019 0.001 PHE A2052 TYR 0.019 0.001 TYR F 367 ARG 0.003 0.000 ARG E 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 VAL cc_start: 0.9075 (p) cc_final: 0.8791 (m) REVERT: A 240 MET cc_start: 0.7925 (ttp) cc_final: 0.7127 (ttt) REVERT: A 244 MET cc_start: 0.8319 (mtp) cc_final: 0.7872 (mtp) REVERT: A 290 ILE cc_start: 0.9206 (mm) cc_final: 0.8969 (pt) REVERT: A 363 MET cc_start: 0.7492 (mtt) cc_final: 0.6729 (ptm) REVERT: A 384 MET cc_start: 0.6665 (tpp) cc_final: 0.6335 (tpt) REVERT: A 435 MET cc_start: 0.8675 (mmm) cc_final: 0.8291 (tmm) REVERT: A 569 MET cc_start: 0.7814 (tpt) cc_final: 0.7609 (mmm) REVERT: A 749 MET cc_start: 0.7888 (tpp) cc_final: 0.7604 (mmt) REVERT: A 812 PHE cc_start: 0.8867 (t80) cc_final: 0.8647 (t80) REVERT: A 1341 MET cc_start: 0.8244 (mmm) cc_final: 0.7991 (mmt) REVERT: A 1447 GLN cc_start: 0.8436 (mm110) cc_final: 0.7985 (tm-30) REVERT: A 1520 MET cc_start: 0.8225 (tpp) cc_final: 0.7976 (tpp) REVERT: A 1607 MET cc_start: 0.7593 (mpp) cc_final: 0.7286 (mpp) REVERT: A 1642 LEU cc_start: 0.8611 (tt) cc_final: 0.8031 (tt) REVERT: A 1815 MET cc_start: 0.9052 (pmm) cc_final: 0.8415 (pmm) REVERT: A 1923 LEU cc_start: 0.8660 (pt) cc_final: 0.8066 (pp) REVERT: A 1973 LEU cc_start: 0.8093 (tt) cc_final: 0.7560 (mp) REVERT: A 2162 PHE cc_start: 0.7003 (m-80) cc_final: 0.6789 (m-80) REVERT: B 237 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8586 (mt-10) REVERT: B 258 VAL cc_start: 0.8690 (t) cc_final: 0.8480 (m) REVERT: C 236 LEU cc_start: 0.7694 (mt) cc_final: 0.7418 (mt) REVERT: C 242 ARG cc_start: 0.8988 (tpp80) cc_final: 0.8744 (tpt170) REVERT: C 270 MET cc_start: 0.8617 (mtm) cc_final: 0.8186 (pmm) REVERT: D 264 MET cc_start: 0.8182 (tmm) cc_final: 0.7832 (tpt) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.3021 time to fit residues: 115.5977 Evaluate side-chains 190 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 179 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 213 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN A1319 ASN A1338 GLN ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1850 GLN ** A1920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18109 Z= 0.254 Angle : 0.744 14.319 24561 Z= 0.374 Chirality : 0.043 0.194 2898 Planarity : 0.005 0.049 3087 Dihedral : 5.920 70.025 2409 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.60 % Favored : 86.40 % Rotamer: Outliers : 0.40 % Allowed : 2.79 % Favored : 96.82 % 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: -1.57 (0.18), residues: 2193 helix: 0.70 (0.14), residues: 1334 sheet: -2.44 (0.57), residues: 72 loop : -4.19 (0.18), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 113 HIS 0.007 0.001 HIS A1622 PHE 0.020 0.002 PHE A2052 TYR 0.019 0.002 TYR A 85 ARG 0.011 0.001 ARG A1647 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8269 (ttt) cc_final: 0.8066 (mtp) REVERT: A 240 MET cc_start: 0.7895 (ttp) cc_final: 0.7002 (ttt) REVERT: A 244 MET cc_start: 0.8374 (mtp) cc_final: 0.7947 (mtp) REVERT: A 384 MET cc_start: 0.6541 (tpp) cc_final: 0.6124 (tpt) REVERT: A 435 MET cc_start: 0.8678 (mmm) cc_final: 0.8383 (tmm) REVERT: A 569 MET cc_start: 0.7764 (tpt) cc_final: 0.7519 (mmm) REVERT: A 1447 GLN cc_start: 0.8467 (mm110) cc_final: 0.7960 (tm-30) REVERT: A 1483 LYS cc_start: 0.6451 (pptt) cc_final: 0.6194 (pptt) REVERT: A 1520 MET cc_start: 0.8289 (tpp) cc_final: 0.8033 (tpp) REVERT: A 1607 MET cc_start: 0.7569 (mpp) cc_final: 0.7236 (mpp) REVERT: A 1613 LYS cc_start: 0.9163 (tttt) cc_final: 0.8779 (tptt) REVERT: A 1920 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7679 (tm-30) REVERT: A 1973 LEU cc_start: 0.8094 (tt) cc_final: 0.7621 (mp) REVERT: A 2162 PHE cc_start: 0.7178 (m-80) cc_final: 0.6917 (m-80) REVERT: B 237 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8590 (mt-10) REVERT: B 258 VAL cc_start: 0.8739 (t) cc_final: 0.8500 (m) REVERT: C 236 LEU cc_start: 0.7659 (mt) cc_final: 0.7405 (mt) REVERT: C 242 ARG cc_start: 0.9012 (tpp80) cc_final: 0.8723 (tpt170) REVERT: C 270 MET cc_start: 0.8720 (mtm) cc_final: 0.8009 (pmm) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.3011 time to fit residues: 108.7681 Evaluate side-chains 179 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1027 ASN A1338 GLN ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1850 GLN A1898 ASN ** A1920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18109 Z= 0.190 Angle : 0.710 13.933 24561 Z= 0.350 Chirality : 0.042 0.228 2898 Planarity : 0.005 0.058 3087 Dihedral : 5.693 69.720 2409 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 0.40 % Allowed : 1.89 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.18), residues: 2193 helix: 0.98 (0.15), residues: 1325 sheet: -2.43 (0.56), residues: 75 loop : -4.03 (0.18), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1738 HIS 0.007 0.001 HIS A1622 PHE 0.019 0.001 PHE A 235 TYR 0.017 0.001 TYR F 367 ARG 0.007 0.000 ARG A1647 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.7993 (tp) cc_final: 0.7344 (pp) REVERT: A 64 VAL cc_start: 0.9061 (p) cc_final: 0.8822 (m) REVERT: A 187 MET cc_start: 0.8345 (ttt) cc_final: 0.8049 (mtp) REVERT: A 240 MET cc_start: 0.7859 (ttp) cc_final: 0.7038 (ttt) REVERT: A 244 MET cc_start: 0.8330 (mtp) cc_final: 0.7857 (mtp) REVERT: A 363 MET cc_start: 0.7291 (mtt) cc_final: 0.6810 (ptm) REVERT: A 384 MET cc_start: 0.6660 (tpp) cc_final: 0.6336 (tpt) REVERT: A 435 MET cc_start: 0.8656 (mmm) cc_final: 0.8312 (tmm) REVERT: A 569 MET cc_start: 0.7874 (tpt) cc_final: 0.7620 (mmm) REVERT: A 693 PHE cc_start: 0.8126 (m-80) cc_final: 0.7850 (m-10) REVERT: A 812 PHE cc_start: 0.8698 (t80) cc_final: 0.8382 (t80) REVERT: A 1447 GLN cc_start: 0.8462 (mm110) cc_final: 0.8068 (tm-30) REVERT: A 1480 MET cc_start: 0.7197 (pmm) cc_final: 0.6954 (pmm) REVERT: A 1520 MET cc_start: 0.8075 (tpp) cc_final: 0.7843 (tpp) REVERT: A 1607 MET cc_start: 0.7650 (mpp) cc_final: 0.7314 (mpp) REVERT: A 1613 LYS cc_start: 0.9139 (tttt) cc_final: 0.8731 (tptt) REVERT: A 1815 MET cc_start: 0.9055 (pmm) cc_final: 0.8367 (pmm) REVERT: A 1920 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7676 (tm-30) REVERT: A 1973 LEU cc_start: 0.8126 (tt) cc_final: 0.7610 (mp) REVERT: A 2162 PHE cc_start: 0.7190 (m-80) cc_final: 0.6963 (m-80) REVERT: B 237 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8443 (mt-10) REVERT: B 258 VAL cc_start: 0.8668 (t) cc_final: 0.8455 (m) REVERT: C 236 LEU cc_start: 0.7584 (mt) cc_final: 0.7026 (mt) REVERT: C 242 ARG cc_start: 0.9015 (tpp80) cc_final: 0.8756 (tpt170) REVERT: C 270 MET cc_start: 0.8677 (mtm) cc_final: 0.8175 (pmm) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2999 time to fit residues: 114.1689 Evaluate side-chains 188 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 0.0570 chunk 179 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1622 HIS A1850 GLN ** A1920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18109 Z= 0.189 Angle : 0.706 13.267 24561 Z= 0.347 Chirality : 0.042 0.266 2898 Planarity : 0.005 0.052 3087 Dihedral : 5.590 69.578 2409 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.40 % Favored : 87.60 % Rotamer: Outliers : 0.40 % Allowed : 1.00 % Favored : 98.61 % 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: -1.17 (0.18), residues: 2193 helix: 0.98 (0.15), residues: 1339 sheet: -2.37 (0.59), residues: 71 loop : -3.95 (0.19), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1738 HIS 0.004 0.001 HIS A1539 PHE 0.019 0.001 PHE A 829 TYR 0.014 0.001 TYR A 838 ARG 0.005 0.000 ARG A1647 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.7869 (tp) cc_final: 0.7375 (pp) REVERT: A 11 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7537 (mp0) REVERT: A 64 VAL cc_start: 0.9031 (p) cc_final: 0.8787 (m) REVERT: A 187 MET cc_start: 0.8239 (ttt) cc_final: 0.7991 (ttt) REVERT: A 240 MET cc_start: 0.7905 (ttp) cc_final: 0.7152 (ttt) REVERT: A 244 MET cc_start: 0.8320 (mtp) cc_final: 0.7869 (mtp) REVERT: A 363 MET cc_start: 0.7337 (mtt) cc_final: 0.6983 (ptm) REVERT: A 384 MET cc_start: 0.6637 (tpp) cc_final: 0.6309 (tpt) REVERT: A 435 MET cc_start: 0.8646 (mmm) cc_final: 0.8299 (tmm) REVERT: A 569 MET cc_start: 0.7885 (tpt) cc_final: 0.7627 (mmm) REVERT: A 812 PHE cc_start: 0.8692 (t80) cc_final: 0.8358 (t80) REVERT: A 1447 GLN cc_start: 0.8447 (mm110) cc_final: 0.7921 (tm-30) REVERT: A 1480 MET cc_start: 0.7187 (pmm) cc_final: 0.6934 (pmm) REVERT: A 1520 MET cc_start: 0.8084 (tpp) cc_final: 0.7821 (tpp) REVERT: A 1607 MET cc_start: 0.7648 (mpp) cc_final: 0.7286 (mpp) REVERT: A 1613 LYS cc_start: 0.9128 (tttt) cc_final: 0.8766 (tptt) REVERT: A 1784 TRP cc_start: 0.8588 (p90) cc_final: 0.8072 (p90) REVERT: A 1920 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7762 (tm-30) REVERT: A 1973 LEU cc_start: 0.8138 (tt) cc_final: 0.7622 (mp) REVERT: B 237 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8625 (mt-10) REVERT: C 236 LEU cc_start: 0.7979 (mt) cc_final: 0.7096 (mt) REVERT: C 242 ARG cc_start: 0.9003 (tpp80) cc_final: 0.8741 (tpt170) REVERT: C 270 MET cc_start: 0.8674 (mtm) cc_final: 0.8056 (pmm) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.3080 time to fit residues: 115.9480 Evaluate side-chains 192 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 145 optimal weight: 0.0970 chunk 220 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1850 GLN A1898 ASN ** A1920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18109 Z= 0.261 Angle : 0.758 13.382 24561 Z= 0.380 Chirality : 0.044 0.249 2898 Planarity : 0.005 0.051 3087 Dihedral : 5.875 70.053 2409 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer: Outliers : 0.40 % Allowed : 0.65 % Favored : 98.96 % 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: -1.37 (0.18), residues: 2193 helix: 0.83 (0.14), residues: 1338 sheet: -2.47 (0.59), residues: 71 loop : -4.05 (0.18), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 113 HIS 0.007 0.001 HIS A1392 PHE 0.020 0.002 PHE A2052 TYR 0.019 0.002 TYR A 85 ARG 0.007 0.001 ARG A1647 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.7949 (tp) cc_final: 0.7377 (pp) REVERT: A 11 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7478 (mp0) REVERT: A 187 MET cc_start: 0.8255 (ttt) cc_final: 0.7834 (ttt) REVERT: A 240 MET cc_start: 0.7764 (ttp) cc_final: 0.6696 (ttt) REVERT: A 244 MET cc_start: 0.8297 (mtp) cc_final: 0.7903 (mtp) REVERT: A 384 MET cc_start: 0.6395 (tpp) cc_final: 0.5985 (tpt) REVERT: A 435 MET cc_start: 0.8671 (mmm) cc_final: 0.8336 (tmm) REVERT: A 569 MET cc_start: 0.7817 (tpt) cc_final: 0.7542 (mmm) REVERT: A 1447 GLN cc_start: 0.8465 (mm110) cc_final: 0.7947 (tm-30) REVERT: A 1520 MET cc_start: 0.8174 (tpp) cc_final: 0.7953 (tpp) REVERT: A 1607 MET cc_start: 0.7575 (mpp) cc_final: 0.7196 (mpp) REVERT: A 1684 ARG cc_start: 0.6565 (mtt180) cc_final: 0.6252 (mtt180) REVERT: A 1920 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7961 (tm-30) REVERT: A 1973 LEU cc_start: 0.8114 (tt) cc_final: 0.7694 (mp) REVERT: B 237 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8716 (mt-10) REVERT: B 258 VAL cc_start: 0.8717 (t) cc_final: 0.8471 (m) REVERT: C 236 LEU cc_start: 0.7528 (mt) cc_final: 0.7188 (mt) REVERT: C 242 ARG cc_start: 0.9054 (tpp80) cc_final: 0.8750 (tpt170) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3091 time to fit residues: 110.6412 Evaluate side-chains 184 residues out of total 1978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 161 optimal weight: 0.0670 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1850 GLN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 GLN ** 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 = 0.3608 r_free = 0.3608 target = 0.075050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.059056 restraints weight = 578796.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.063162 restraints weight = 232003.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.063641 restraints weight = 111914.894| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18109 Z= 0.191 Angle : 0.722 13.517 24561 Z= 0.355 Chirality : 0.042 0.257 2898 Planarity : 0.005 0.052 3087 Dihedral : 5.681 69.654 2409 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % Rotamer: Outliers : 0.40 % Allowed : 0.65 % Favored : 98.96 % 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: -1.18 (0.18), residues: 2193 helix: 0.96 (0.15), residues: 1338 sheet: -2.35 (0.60), residues: 66 loop : -3.93 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A1738 HIS 0.003 0.001 HIS A1804 PHE 0.019 0.001 PHE A2052 TYR 0.025 0.001 TYR F 367 ARG 0.008 0.000 ARG A1647 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3534.46 seconds wall clock time: 66 minutes 34.29 seconds (3994.29 seconds total)