Starting phenix.real_space_refine on Sat Feb 17 06:57:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v85_21095/02_2024/6v85_21095.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v85_21095/02_2024/6v85_21095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v85_21095/02_2024/6v85_21095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v85_21095/02_2024/6v85_21095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v85_21095/02_2024/6v85_21095.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v85_21095/02_2024/6v85_21095.pdb" } resolution = 4.38 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 11421 2.51 5 N 3050 2.21 5 O 3308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 56": "OE1" <-> "OE2" 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 GLU 246": "OE1" <-> "OE2" Residue "A ARG 311": "NH1" <-> "NH2" 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 ARG 929": "NH1" <-> "NH2" Residue "A ARG 984": "NH1" <-> "NH2" Residue "A ARG 1047": "NH1" <-> "NH2" Residue "A ARG 1052": "NH1" <-> "NH2" Residue "A GLU 1053": "OE1" <-> "OE2" 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 GLU 1182": "OE1" <-> "OE2" Residue "A ARG 1207": "NH1" <-> "NH2" Residue "A ARG 1220": "NH1" <-> "NH2" Residue "A GLU 1361": "OE1" <-> "OE2" Residue "A ARG 1446": "NH1" <-> "NH2" Residue "A TYR 1565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1741": "OE1" <-> "OE2" Residue "A ARG 1792": "NH1" <-> "NH2" Residue "A PHE 1956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1969": "NH1" <-> "NH2" Residue "A GLU 2083": "OE1" <-> "OE2" Residue "A ARG 2175": "NH1" <-> "NH2" Residue "B GLU 268": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17878 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 15200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1901, 15200 Classifications: {'peptide': 1901} Link IDs: {'PTRANS': 84, 'TRANS': 1816} Chain breaks: 28 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: "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: "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 8264 SG CYS A1136 113.479 58.500 106.151 1.00 75.09 S ATOM 10033 SG CYS A1373 114.339 55.329 104.362 1.00105.67 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: 10.98, per 1000 atoms: 0.61 Number of scatterers: 17878 At special positions: 0 Unit cell: (184.8, 143.36, 140, 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 3308 8.00 N 3050 7.00 C 11421 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: 7.16 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A1368 " pdb=" ZN A3002 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1136 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1373 " 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4294 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 7 sheets defined 62.7% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 removed outlier: 3.658A pdb=" N TYR A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 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: 3.668A pdb=" N LYS A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ALA A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLY A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 174 through 197 Processing helix chain 'A' and resid 235 through 257 removed outlier: 3.590A pdb=" N VAL A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 283 removed outlier: 3.969A pdb=" N LYS A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 302 removed outlier: 4.061A pdb=" N ASN A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 328 removed outlier: 3.982A 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 Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.791A pdb=" N ALA A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 415 Processing helix chain 'A' and resid 427 through 437 removed outlier: 3.596A pdb=" N LEU A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.944A pdb=" N LYS A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 527 through 534 removed outlier: 3.515A pdb=" N GLN A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 583 Processing helix chain 'A' and resid 584 through 587 Processing helix chain 'A' and resid 597 through 611 Processing helix chain 'A' and resid 665 through 671 removed outlier: 3.664A pdb=" N GLN A 670 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TRP A 671 " --> pdb=" O CYS A 668 " (cutoff:3.500A) 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 702 removed outlier: 3.954A pdb=" N LEU A 698 " --> pdb=" O GLU A 694 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 761 removed outlier: 4.143A pdb=" N TRP A 747 " --> pdb=" O CYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 815 Processing helix chain 'A' and resid 846 through 851 Processing helix chain 'A' and resid 863 through 881 removed outlier: 3.667A pdb=" N ASN A 881 " --> pdb=" O ARG A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 905 removed outlier: 3.502A pdb=" N CYS A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 923 removed outlier: 3.575A pdb=" N ASN A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 932 removed outlier: 4.352A 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 Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 990 through 997 removed outlier: 3.663A pdb=" N ASP A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1023 removed outlier: 3.896A pdb=" N ALA A1012 " --> pdb=" O PRO A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1034 Processing helix chain 'A' and resid 1035 through 1036 No H-bonds generated for 'chain 'A' and resid 1035 through 1036' Processing helix chain 'A' and resid 1037 through 1051 Processing helix chain 'A' and resid 1056 through 1067 Processing helix chain 'A' and resid 1067 through 1078 removed outlier: 3.545A 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 Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1124 through 1132 removed outlier: 3.659A pdb=" N LYS A1129 " --> pdb=" O PRO A1125 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A1132 " --> pdb=" O LEU A1128 " (cutoff:3.500A) 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 1237 through 1250 removed outlier: 3.770A pdb=" N ALA A1241 " --> pdb=" O SER A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1271 Processing helix chain 'A' and resid 1333 through 1352 Processing helix chain 'A' and resid 1438 through 1452 Processing helix chain 'A' and resid 1485 through 1502 Processing helix chain 'A' and resid 1510 through 1523 removed outlier: 3.776A pdb=" N ILE A1514 " --> pdb=" O GLY A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1537 removed outlier: 4.448A pdb=" N ALA A1529 " --> pdb=" O ILE A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1549 removed outlier: 3.834A pdb=" N ARG A1544 " --> pdb=" O PRO A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1586 removed outlier: 4.009A pdb=" N VAL A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A1586 " --> pdb=" O ASN A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1605 through 1624 Processing helix chain 'A' and resid 1636 through 1649 Processing helix chain 'A' and resid 1650 through 1652 No H-bonds generated for 'chain 'A' and resid 1650 through 1652' Processing helix chain 'A' and resid 1658 through 1665 removed outlier: 3.840A pdb=" N ASN A1662 " --> pdb=" O GLU A1658 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET A1664 " --> pdb=" O LEU A1660 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A1665 " --> pdb=" O SER A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1690 Processing helix chain 'A' and resid 1697 through 1701 Processing helix chain 'A' and resid 1768 through 1775 removed outlier: 4.090A pdb=" N HIS A1771 " --> pdb=" O ALA A1768 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR A1773 " --> pdb=" O SER A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1796 Processing helix chain 'A' and resid 1814 through 1822 removed outlier: 4.138A pdb=" N ILE A1818 " --> pdb=" O SER A1814 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A1819 " --> pdb=" O MET A1815 " (cutoff:3.500A) Processing helix chain 'A' and resid 1848 through 1862 removed outlier: 4.160A pdb=" N ILE A1852 " --> pdb=" O PRO A1848 " (cutoff:3.500A) Proline residue: A1856 - end of helix removed outlier: 4.497A pdb=" N ALA A1862 " --> pdb=" O LYS A1858 " (cutoff:3.500A) Processing helix chain 'A' and resid 1890 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 Processing helix chain 'A' and resid 2021 through 2045 removed outlier: 4.077A pdb=" N GLN A2025 " --> pdb=" O GLU A2021 " (cutoff:3.500A) Processing helix chain 'A' and resid 2053 through 2061 removed outlier: 3.929A pdb=" N ILE A2060 " --> pdb=" O ASP A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2083 through 2104 Processing helix chain 'A' and resid 2126 through 2144 Processing helix chain 'A' and resid 2145 through 2147 No H-bonds generated for 'chain 'A' and resid 2145 through 2147' Processing helix chain 'A' and resid 2149 through 2161 removed outlier: 3.716A pdb=" N ARG A2153 " --> pdb=" O PRO A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2170 through 2175 removed outlier: 3.655A pdb=" N SER A2173 " --> pdb=" O ILE A2170 " (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: 3.554A pdb=" N HIS A2226 " --> pdb=" O VAL A2222 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 358 Processing helix chain 'F' and resid 360 through 374 removed outlier: 3.620A pdb=" N GLN F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 390 Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 205 through 270 removed outlier: 4.550A pdb=" N SER B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 271 removed outlier: 3.513A pdb=" N LEU C 205 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'D' and resid 205 through 270 removed outlier: 4.551A pdb=" N SER D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE D 250 " --> pdb=" O SER D 246 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN D 251 " --> pdb=" O GLN D 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 270 removed outlier: 3.511A pdb=" N LEU E 205 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN E 218 " --> pdb=" O SER E 214 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER E 248 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN E 251 " --> pdb=" O GLN E 247 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 207 removed outlier: 4.015A pdb=" N ILE A 214 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 765 through 771 removed outlier: 3.799A pdb=" N ARG A 765 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER A 658 " --> pdb=" O VAL A 779 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 704 through 705 Processing sheet with id=AA4, first strand: chain 'A' and resid 829 through 832 Processing sheet with id=AA5, first strand: chain 'A' and resid 1173 through 1176 removed outlier: 3.817A pdb=" N THR A1192 " --> pdb=" O LEU A1367 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TRP A1193 " --> pdb=" O SER A1318 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A1318 " --> pdb=" O TRP A1193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1593 through 1594 Processing sheet with id=AA7, first strand: chain 'A' and resid 1828 through 1829 removed outlier: 7.207A pdb=" N LEU A1805 " --> pdb=" O HIS A1909 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N ASP A1911 " --> pdb=" O LEU A1805 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A1908 " --> pdb=" O ILE A1945 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LYS A1947 " --> pdb=" O VAL A1908 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL A1910 " --> pdb=" O LYS A1947 " (cutoff:3.500A) 1028 hydrogen bonds defined for protein. 2986 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.73 Time building geometry restraints manager: 7.58 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: 5548 1.34 - 1.46: 3121 1.46 - 1.58: 9384 1.58 - 1.70: 0 1.70 - 1.82: 154 Bond restraints: 18207 Sorted by residual: bond pdb=" N TRP A1738 " pdb=" CA TRP A1738 " ideal model delta sigma weight residual 1.457 1.503 -0.045 1.29e-02 6.01e+03 1.23e+01 bond pdb=" N ILE A1739 " pdb=" CA ILE A1739 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N GLU A1134 " pdb=" CA GLU A1134 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.55e+00 bond pdb=" N ILE A1740 " pdb=" CA ILE A1740 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.53e+00 bond pdb=" N ILE A1970 " pdb=" CA ILE A1970 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.24e-02 6.50e+03 9.13e+00 ... (remaining 18202 not shown) Histogram of bond angle deviations from ideal: 92.26 - 100.67: 26 100.67 - 109.08: 1281 109.08 - 117.49: 12579 117.49 - 125.90: 10531 125.90 - 134.31: 274 Bond angle restraints: 24691 Sorted by residual: angle pdb=" C CYS A1374 " pdb=" N VAL A1375 " pdb=" CA VAL A1375 " ideal model delta sigma weight residual 122.97 129.97 -7.00 9.80e-01 1.04e+00 5.10e+01 angle pdb=" O VAL A1375 " pdb=" C VAL A1375 " pdb=" N ARG A1376 " ideal model delta sigma weight residual 121.85 126.95 -5.10 7.60e-01 1.73e+00 4.51e+01 angle pdb=" N VAL A2045 " pdb=" CA VAL A2045 " pdb=" C VAL A2045 " ideal model delta sigma weight residual 112.98 106.33 6.65 1.25e+00 6.40e-01 2.83e+01 angle pdb=" N VAL A1375 " pdb=" CA VAL A1375 " pdb=" C VAL A1375 " ideal model delta sigma weight residual 111.48 106.53 4.95 9.40e-01 1.13e+00 2.77e+01 angle pdb=" CA ILE A1138 " pdb=" C ILE A1138 " pdb=" O ILE A1138 " ideal model delta sigma weight residual 121.27 116.56 4.71 1.04e+00 9.25e-01 2.05e+01 ... (remaining 24686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 9862 18.00 - 35.99: 1017 35.99 - 53.99: 155 53.99 - 71.99: 13 71.99 - 89.99: 16 Dihedral angle restraints: 11063 sinusoidal: 4457 harmonic: 6606 Sorted by residual: dihedral pdb=" CA LEU A1563 " pdb=" C LEU A1563 " pdb=" N ASP A1564 " pdb=" CA ASP A1564 " ideal model delta harmonic sigma weight residual -180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA TYR A 260 " pdb=" C TYR A 260 " pdb=" N LEU A 261 " pdb=" CA LEU A 261 " ideal model delta harmonic sigma weight residual -180.00 -155.31 -24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA LEU A2148 " pdb=" C LEU A2148 " pdb=" N PRO A2149 " pdb=" CA PRO A2149 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 11060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2554 0.076 - 0.152: 320 0.152 - 0.229: 27 0.229 - 0.305: 6 0.305 - 0.381: 3 Chirality restraints: 2910 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 2.26 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA HIS A 415 " pdb=" N HIS A 415 " pdb=" C HIS A 415 " pdb=" CB HIS A 415 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA ASN A1743 " pdb=" N ASN A1743 " pdb=" C ASN A1743 " pdb=" CB ASN A1743 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 2907 not shown) Planarity restraints: 3105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A1367 " 0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C LEU A1367 " -0.069 2.00e-02 2.50e+03 pdb=" O LEU A1367 " 0.026 2.00e-02 2.50e+03 pdb=" N HIS A1368 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 98 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO A 99 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1950 " -0.023 2.00e-02 2.50e+03 1.70e-02 7.23e+00 pdb=" CG TRP A1950 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A1950 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A1950 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1950 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1950 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A1950 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1950 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1950 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A1950 " 0.000 2.00e-02 2.50e+03 ... (remaining 3102 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 347 2.64 - 3.21: 18676 3.21 - 3.77: 27486 3.77 - 4.34: 35375 4.34 - 4.90: 55536 Nonbonded interactions: 137420 Sorted by model distance: nonbonded pdb=" O ASN A1743 " pdb=" ND2 ASN A1743 " model vdw 2.077 2.520 nonbonded pdb=" NE1 TRP A1193 " pdb=" OG SER A1318 " model vdw 2.091 2.520 nonbonded pdb=" O MET A2006 " pdb=" OG1 THR A2009 " model vdw 2.117 2.440 nonbonded pdb=" NZ LYS A1765 " pdb=" O ASN A1982 " model vdw 2.129 2.520 nonbonded pdb=" OE2 GLU A 880 " pdb=" OG SER A1307 " model vdw 2.140 2.440 ... (remaining 137415 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=0.26 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: 3.500 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: 10.430 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 57.320 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 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:3.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 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 : 0.006 0.060 18207 Z= 0.371 Angle : 0.886 10.919 24691 Z= 0.522 Chirality : 0.052 0.381 2910 Planarity : 0.005 0.070 3105 Dihedral : 14.459 89.986 6769 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.41 % Allowed : 13.54 % Favored : 86.05 % Rotamer: Outliers : 0.45 % Allowed : 8.67 % Favored : 90.89 % Cbeta Deviations : 0.09 % 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: -3.59 (0.15), residues: 2204 helix: -1.09 (0.12), residues: 1293 sheet: -3.04 (0.48), residues: 88 loop : -4.50 (0.17), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A1950 HIS 0.010 0.002 HIS A1368 PHE 0.024 0.002 PHE A1311 TYR 0.021 0.002 TYR A1793 ARG 0.006 0.001 ARG A1974 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 302 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8200 (pt) cc_final: 0.7787 (pp) REVERT: A 55 GLU cc_start: 0.8996 (tp30) cc_final: 0.8370 (tp30) REVERT: A 209 ARG cc_start: 0.8277 (tpt170) cc_final: 0.8004 (ttp80) REVERT: A 236 GLU cc_start: 0.8648 (mp0) cc_final: 0.8201 (mp0) REVERT: A 363 MET cc_start: 0.7372 (ttp) cc_final: 0.6939 (ttm) REVERT: A 399 LEU cc_start: 0.9181 (tp) cc_final: 0.8979 (tp) REVERT: A 421 LEU cc_start: 0.0360 (OUTLIER) cc_final: 0.0059 (tp) REVERT: A 612 ILE cc_start: 0.7462 (tp) cc_final: 0.7214 (tp) REVERT: A 689 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7281 (p90) REVERT: A 767 MET cc_start: 0.8127 (tpp) cc_final: 0.7860 (mmm) REVERT: A 775 GLN cc_start: 0.7477 (pt0) cc_final: 0.7212 (pt0) REVERT: A 830 PHE cc_start: 0.7962 (t80) cc_final: 0.7589 (t80) REVERT: A 891 LEU cc_start: 0.9266 (tp) cc_final: 0.8919 (tt) REVERT: A 947 ARG cc_start: 0.8047 (mtt180) cc_final: 0.7827 (mtt180) REVERT: A 1111 LEU cc_start: 0.9259 (mt) cc_final: 0.8871 (mt) REVERT: A 1828 TYR cc_start: 0.7735 (m-10) cc_final: 0.7257 (m-80) REVERT: A 1920 GLN cc_start: 0.6449 (tt0) cc_final: 0.6074 (tt0) REVERT: F 362 LYS cc_start: 0.8764 (mttt) cc_final: 0.8482 (ttmm) REVERT: F 387 ILE cc_start: 0.8868 (mm) cc_final: 0.8646 (mm) REVERT: C 218 ASN cc_start: 0.0665 (m-40) cc_final: 0.0099 (m110) REVERT: C 233 MET cc_start: 0.6365 (mtp) cc_final: 0.5841 (mtm) REVERT: C 247 GLN cc_start: 0.7851 (mm110) cc_final: 0.6966 (pp30) REVERT: C 252 THR cc_start: 0.6561 (p) cc_final: 0.6001 (m) REVERT: C 264 MET cc_start: 0.7478 (ttm) cc_final: 0.7066 (ttm) REVERT: D 249 LEU cc_start: 0.7954 (mt) cc_final: 0.7669 (pp) REVERT: D 270 MET cc_start: 0.5900 (mtt) cc_final: 0.5189 (tpt) outliers start: 9 outliers final: 4 residues processed: 309 average time/residue: 0.3042 time to fit residues: 141.0020 Evaluate side-chains 211 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 205 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 174 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 104 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS A 368 HIS A 403 HIS A 531 GLN A 583 HIS A 591 ASN A 774 ASN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN A 870 ASN A 925 HIS A1107 ASN A1272 ASN A1289 ASN ** A1338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1339 GLN A1366 HIS A1368 HIS A1447 GLN ** A1659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1688 ASN ** A1850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1898 ASN A1919 ASN A1920 GLN A2024 ASN A2025 GLN ** A2057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2144 ASN F 372 ASN F 379 GLN B 234 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18207 Z= 0.300 Angle : 0.771 11.389 24691 Z= 0.397 Chirality : 0.045 0.341 2910 Planarity : 0.006 0.082 3105 Dihedral : 6.238 86.696 2425 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.29 % Favored : 87.62 % Rotamer: Outliers : 0.20 % Allowed : 6.19 % Favored : 93.61 % 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: -1.93 (0.18), residues: 2204 helix: 0.42 (0.14), residues: 1307 sheet: -2.64 (0.51), residues: 88 loop : -4.18 (0.18), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A1950 HIS 0.007 0.001 HIS A1539 PHE 0.021 0.002 PHE A 69 TYR 0.022 0.002 TYR A1793 ARG 0.007 0.001 ARG A1376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 276 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8241 (pt) cc_final: 0.7831 (pp) REVERT: A 55 GLU cc_start: 0.8770 (tp30) cc_final: 0.8452 (tp30) REVERT: A 209 ARG cc_start: 0.8231 (tpt170) cc_final: 0.7987 (ttp80) REVERT: A 236 GLU cc_start: 0.8731 (mp0) cc_final: 0.8173 (mp0) REVERT: A 245 TYR cc_start: 0.8478 (m-10) cc_final: 0.8128 (m-80) REVERT: A 399 LEU cc_start: 0.9059 (tp) cc_final: 0.8837 (tp) REVERT: A 777 ILE cc_start: 0.9103 (mp) cc_final: 0.8553 (mp) REVERT: A 830 PHE cc_start: 0.7917 (t80) cc_final: 0.7599 (t80) REVERT: A 891 LEU cc_start: 0.9250 (tp) cc_final: 0.8666 (tt) REVERT: A 1111 LEU cc_start: 0.9189 (mt) cc_final: 0.8830 (mt) REVERT: A 1249 TYR cc_start: 0.8114 (t80) cc_final: 0.7898 (t80) REVERT: A 1366 HIS cc_start: 0.6037 (OUTLIER) cc_final: 0.5760 (t-170) REVERT: A 1520 MET cc_start: 0.8296 (mmm) cc_final: 0.7830 (tmm) REVERT: F 362 LYS cc_start: 0.8818 (mttt) cc_final: 0.8615 (ttmm) REVERT: F 382 ASP cc_start: 0.8702 (m-30) cc_final: 0.8471 (m-30) REVERT: B 254 LYS cc_start: 0.8276 (tptt) cc_final: 0.7567 (tppp) REVERT: C 233 MET cc_start: 0.6066 (mtp) cc_final: 0.5389 (mtm) REVERT: C 247 GLN cc_start: 0.8258 (mm110) cc_final: 0.7254 (pp30) REVERT: C 271 ILE cc_start: 0.6406 (mm) cc_final: 0.6179 (mm) REVERT: D 249 LEU cc_start: 0.8126 (mt) cc_final: 0.7893 (pp) REVERT: D 270 MET cc_start: 0.6282 (mtt) cc_final: 0.5436 (tpt) outliers start: 4 outliers final: 1 residues processed: 280 average time/residue: 0.3149 time to fit residues: 132.3236 Evaluate side-chains 213 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 211 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 55 optimal weight: 0.0770 chunk 201 optimal weight: 9.9990 chunk 218 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 208 ASN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN A 531 GLN A 870 ASN ** A1209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 ASN ** A1338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1659 ASN A1850 GLN A1920 GLN A2057 ASN A2212 GLN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 ASN D 228 ASN A Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18207 Z= 0.202 Angle : 0.696 11.374 24691 Z= 0.354 Chirality : 0.043 0.292 2910 Planarity : 0.005 0.084 3105 Dihedral : 5.905 89.592 2425 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.54 % Favored : 89.36 % Rotamer: Outliers : 0.05 % Allowed : 4.90 % Favored : 95.05 % 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: -1.09 (0.18), residues: 2204 helix: 1.16 (0.14), residues: 1309 sheet: -2.36 (0.51), residues: 91 loop : -3.95 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A1950 HIS 0.006 0.001 HIS A1539 PHE 0.018 0.001 PHE A 401 TYR 0.020 0.001 TYR A1793 ARG 0.006 0.000 ARG A 877 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 297 time to evaluate : 2.255 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: A 44 LEU cc_start: 0.8136 (pt) cc_final: 0.7759 (pp) REVERT: A 98 ILE cc_start: 0.8397 (tp) cc_final: 0.8023 (mm) REVERT: A 209 ARG cc_start: 0.8283 (tpt170) cc_final: 0.8017 (ttp80) REVERT: A 236 GLU cc_start: 0.8642 (mp0) cc_final: 0.8118 (mp0) REVERT: A 245 TYR cc_start: 0.8537 (m-10) cc_final: 0.8156 (m-80) REVERT: A 384 MET cc_start: 0.8286 (tmm) cc_final: 0.7899 (tmm) REVERT: A 399 LEU cc_start: 0.9186 (tp) cc_final: 0.8954 (tp) REVERT: A 575 ILE cc_start: 0.9541 (mt) cc_final: 0.9209 (tt) REVERT: A 691 HIS cc_start: 0.1281 (m90) cc_final: 0.0949 (m170) REVERT: A 777 ILE cc_start: 0.9138 (mp) cc_final: 0.8925 (mm) REVERT: A 891 LEU cc_start: 0.9179 (tp) cc_final: 0.8519 (tt) REVERT: A 1520 MET cc_start: 0.8222 (mmm) cc_final: 0.7973 (tmm) REVERT: A 2159 ASP cc_start: 0.7751 (m-30) cc_final: 0.7519 (m-30) REVERT: F 362 LYS cc_start: 0.8799 (mttt) cc_final: 0.8418 (ttmm) REVERT: F 363 MET cc_start: 0.8516 (mmm) cc_final: 0.8170 (mmm) REVERT: F 366 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8243 (mm-30) REVERT: F 382 ASP cc_start: 0.8613 (m-30) cc_final: 0.8384 (m-30) REVERT: F 387 ILE cc_start: 0.8947 (mm) cc_final: 0.8732 (mm) REVERT: B 253 ILE cc_start: 0.7979 (mt) cc_final: 0.7682 (mm) REVERT: B 254 LYS cc_start: 0.8416 (tptt) cc_final: 0.7740 (tppp) REVERT: C 233 MET cc_start: 0.6025 (mtp) cc_final: 0.5542 (mtm) REVERT: C 247 GLN cc_start: 0.8155 (mm110) cc_final: 0.7224 (pp30) REVERT: C 261 LYS cc_start: 0.8112 (pttt) cc_final: 0.7847 (pttt) REVERT: D 243 ILE cc_start: 0.7641 (mt) cc_final: 0.7227 (mt) REVERT: D 249 LEU cc_start: 0.8136 (mt) cc_final: 0.7933 (pp) REVERT: D 270 MET cc_start: 0.6348 (mtt) cc_final: 0.5702 (tpt) outliers start: 1 outliers final: 0 residues processed: 298 average time/residue: 0.3330 time to fit residues: 152.4216 Evaluate side-chains 216 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 531 GLN A 573 GLN A 849 ASN A 870 ASN A1209 ASN A1272 ASN ** A1338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1622 HIS A1920 GLN A2057 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18207 Z= 0.211 Angle : 0.683 10.527 24691 Z= 0.349 Chirality : 0.043 0.283 2910 Planarity : 0.005 0.079 3105 Dihedral : 5.777 89.100 2425 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.45 % Favored : 89.50 % Rotamer: Outliers : 0.10 % Allowed : 4.01 % Favored : 95.89 % 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: -0.77 (0.19), residues: 2204 helix: 1.40 (0.15), residues: 1310 sheet: -2.12 (0.51), residues: 91 loop : -3.81 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A1950 HIS 0.005 0.001 HIS A1622 PHE 0.016 0.002 PHE A2052 TYR 0.015 0.001 TYR A2194 ARG 0.004 0.000 ARG D 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 296 time to evaluate : 2.019 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 44 LEU cc_start: 0.8098 (pt) cc_final: 0.7739 (pp) REVERT: A 236 GLU cc_start: 0.8633 (mp0) cc_final: 0.8181 (mp0) REVERT: A 575 ILE cc_start: 0.9553 (mt) cc_final: 0.9230 (tt) REVERT: A 891 LEU cc_start: 0.9217 (tp) cc_final: 0.8556 (tt) REVERT: A 1520 MET cc_start: 0.8230 (mmm) cc_final: 0.7956 (tmm) REVERT: A 1616 LEU cc_start: 0.9008 (pp) cc_final: 0.8804 (tp) REVERT: A 1642 LEU cc_start: 0.8054 (mm) cc_final: 0.7812 (mm) REVERT: A 1920 GLN cc_start: 0.5989 (tt0) cc_final: 0.5671 (tt0) REVERT: A 1962 PHE cc_start: 0.8618 (t80) cc_final: 0.8302 (t80) REVERT: A 2034 GLU cc_start: 0.8457 (pt0) cc_final: 0.7682 (pt0) REVERT: A 2159 ASP cc_start: 0.7921 (m-30) cc_final: 0.7693 (m-30) REVERT: F 362 LYS cc_start: 0.8783 (mttt) cc_final: 0.8470 (ttmm) REVERT: F 363 MET cc_start: 0.8513 (mmm) cc_final: 0.8262 (mmm) REVERT: F 366 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8272 (mm-30) REVERT: F 382 ASP cc_start: 0.8589 (m-30) cc_final: 0.8378 (m-30) REVERT: F 387 ILE cc_start: 0.8932 (mm) cc_final: 0.8729 (mm) REVERT: B 253 ILE cc_start: 0.8004 (mt) cc_final: 0.7774 (mm) REVERT: B 254 LYS cc_start: 0.8454 (tptt) cc_final: 0.7842 (tppp) REVERT: C 261 LYS cc_start: 0.7922 (pttt) cc_final: 0.7591 (pttt) REVERT: D 270 MET cc_start: 0.6163 (mtt) cc_final: 0.5502 (tpt) REVERT: E 242 ARG cc_start: 0.6989 (mtt180) cc_final: 0.6223 (tpt170) outliers start: 2 outliers final: 0 residues processed: 297 average time/residue: 0.3351 time to fit residues: 150.7758 Evaluate side-chains 212 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN A 531 GLN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 ASN A1272 ASN ** A1338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18207 Z= 0.222 Angle : 0.687 10.377 24691 Z= 0.351 Chirality : 0.043 0.321 2910 Planarity : 0.005 0.083 3105 Dihedral : 5.754 89.119 2425 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.64 % Favored : 89.32 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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 (0.19), residues: 2204 helix: 1.43 (0.15), residues: 1310 sheet: -2.25 (0.48), residues: 105 loop : -3.78 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A1950 HIS 0.006 0.001 HIS A1539 PHE 0.021 0.002 PHE A2052 TYR 0.014 0.001 TYR A1397 ARG 0.010 0.000 ARG E 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ILE cc_start: 0.8348 (tp) cc_final: 0.7985 (mm) REVERT: A 236 GLU cc_start: 0.8574 (mp0) cc_final: 0.8171 (mp0) REVERT: A 384 MET cc_start: 0.8260 (tmm) cc_final: 0.7733 (tmm) REVERT: A 399 LEU cc_start: 0.9201 (tp) cc_final: 0.8968 (tp) REVERT: A 575 ILE cc_start: 0.9555 (mt) cc_final: 0.9224 (tt) REVERT: A 891 LEU cc_start: 0.9233 (tp) cc_final: 0.8647 (tt) REVERT: A 1520 MET cc_start: 0.8273 (mmm) cc_final: 0.7957 (tmm) REVERT: A 1616 LEU cc_start: 0.9000 (pp) cc_final: 0.8770 (tp) REVERT: A 1642 LEU cc_start: 0.8013 (mm) cc_final: 0.7772 (mm) REVERT: A 1818 ILE cc_start: 0.9006 (mp) cc_final: 0.8547 (tp) REVERT: A 1962 PHE cc_start: 0.8591 (t80) cc_final: 0.8382 (t80) REVERT: A 2165 PHE cc_start: 0.7021 (t80) cc_final: 0.6699 (t80) REVERT: F 362 LYS cc_start: 0.8785 (mttt) cc_final: 0.8474 (ttmm) REVERT: F 363 MET cc_start: 0.8505 (mmm) cc_final: 0.8263 (mmm) REVERT: F 382 ASP cc_start: 0.8566 (m-30) cc_final: 0.8363 (m-30) REVERT: F 387 ILE cc_start: 0.8942 (mm) cc_final: 0.8739 (mm) REVERT: B 235 GLN cc_start: 0.4868 (mp-120) cc_final: 0.4389 (mm-40) REVERT: B 253 ILE cc_start: 0.7957 (mt) cc_final: 0.7671 (mm) REVERT: B 254 LYS cc_start: 0.8474 (tptt) cc_final: 0.7832 (tppp) REVERT: D 270 MET cc_start: 0.5990 (mtt) cc_final: 0.5353 (tpt) REVERT: E 267 LEU cc_start: 0.6615 (pp) cc_final: 0.6309 (pp) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.3000 time to fit residues: 130.0279 Evaluate side-chains 212 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 125 optimal weight: 0.0070 chunk 52 optimal weight: 0.6980 chunk 214 optimal weight: 3.9990 chunk 178 optimal weight: 0.0670 chunk 99 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN A 531 GLN A 870 ASN ** A1338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1920 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18207 Z= 0.181 Angle : 0.660 10.231 24691 Z= 0.333 Chirality : 0.041 0.220 2910 Planarity : 0.005 0.091 3105 Dihedral : 5.518 86.370 2425 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 0.05 % Allowed : 2.08 % Favored : 97.87 % 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: -0.51 (0.19), residues: 2204 helix: 1.58 (0.15), residues: 1306 sheet: -1.86 (0.51), residues: 101 loop : -3.66 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A1950 HIS 0.005 0.001 HIS A1539 PHE 0.033 0.001 PHE A 69 TYR 0.017 0.001 TYR A2194 ARG 0.009 0.000 ARG E 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 296 time to evaluate : 2.059 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 98 ILE cc_start: 0.8208 (tp) cc_final: 0.7872 (mm) REVERT: A 244 MET cc_start: 0.8390 (ttt) cc_final: 0.7838 (tpp) REVERT: A 370 MET cc_start: 0.8421 (tmm) cc_final: 0.8188 (tmm) REVERT: A 384 MET cc_start: 0.8292 (tmm) cc_final: 0.7883 (tmm) REVERT: A 399 LEU cc_start: 0.9212 (tp) cc_final: 0.8827 (tt) REVERT: A 575 ILE cc_start: 0.9530 (mt) cc_final: 0.9216 (tt) REVERT: A 891 LEU cc_start: 0.9201 (tp) cc_final: 0.8689 (tt) REVERT: A 1520 MET cc_start: 0.8253 (mmm) cc_final: 0.7987 (tmm) REVERT: A 1642 LEU cc_start: 0.8017 (mm) cc_final: 0.7763 (mm) REVERT: A 1818 ILE cc_start: 0.8976 (mp) cc_final: 0.8516 (tp) REVERT: A 1962 PHE cc_start: 0.8566 (t80) cc_final: 0.8229 (t80) REVERT: A 2034 GLU cc_start: 0.8499 (pt0) cc_final: 0.8238 (pt0) REVERT: F 362 LYS cc_start: 0.8749 (mttt) cc_final: 0.8450 (ttmm) REVERT: F 363 MET cc_start: 0.8539 (mmm) cc_final: 0.8300 (mmm) REVERT: F 382 ASP cc_start: 0.8516 (m-30) cc_final: 0.8277 (m-30) REVERT: F 387 ILE cc_start: 0.8865 (mm) cc_final: 0.8663 (mm) REVERT: B 254 LYS cc_start: 0.8429 (tptt) cc_final: 0.7821 (tppp) REVERT: D 249 LEU cc_start: 0.8103 (pp) cc_final: 0.7129 (mm) REVERT: D 270 MET cc_start: 0.5823 (mtt) cc_final: 0.5244 (tpt) outliers start: 1 outliers final: 1 residues processed: 297 average time/residue: 0.3048 time to fit residues: 139.7275 Evaluate side-chains 216 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A 810 ASN A 870 ASN A1272 ASN ** A1338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1920 GLN A1929 ASN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18207 Z= 0.203 Angle : 0.685 13.935 24691 Z= 0.345 Chirality : 0.041 0.194 2910 Planarity : 0.006 0.133 3105 Dihedral : 5.518 86.993 2425 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: -0.42 (0.19), residues: 2204 helix: 1.66 (0.15), residues: 1301 sheet: -1.83 (0.50), residues: 101 loop : -3.57 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A1950 HIS 0.006 0.001 HIS A1539 PHE 0.027 0.002 PHE A 69 TYR 0.014 0.001 TYR A1397 ARG 0.012 0.000 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 2.051 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: A 98 ILE cc_start: 0.8221 (tp) cc_final: 0.7863 (mm) REVERT: A 384 MET cc_start: 0.8358 (tmm) cc_final: 0.8002 (tmm) REVERT: A 399 LEU cc_start: 0.9223 (tp) cc_final: 0.8832 (tt) REVERT: A 575 ILE cc_start: 0.9535 (mt) cc_final: 0.9211 (tt) REVERT: A 891 LEU cc_start: 0.9167 (tp) cc_final: 0.8414 (tt) REVERT: A 895 MET cc_start: 0.8486 (mmm) cc_final: 0.8175 (mmm) REVERT: A 947 ARG cc_start: 0.7586 (ttm170) cc_final: 0.7335 (ttm170) REVERT: A 1342 ILE cc_start: 0.9106 (mm) cc_final: 0.8904 (mm) REVERT: A 1520 MET cc_start: 0.8253 (mmm) cc_final: 0.7965 (tmm) REVERT: A 1962 PHE cc_start: 0.8581 (t80) cc_final: 0.8287 (t80) REVERT: A 2034 GLU cc_start: 0.8499 (pt0) cc_final: 0.8252 (pt0) REVERT: F 362 LYS cc_start: 0.8756 (mttt) cc_final: 0.8452 (ttmm) REVERT: F 363 MET cc_start: 0.8527 (mmm) cc_final: 0.8262 (mmm) REVERT: F 382 ASP cc_start: 0.8518 (m-30) cc_final: 0.8297 (m-30) REVERT: F 387 ILE cc_start: 0.8907 (mm) cc_final: 0.8685 (mm) REVERT: B 233 MET cc_start: 0.5586 (mtp) cc_final: 0.5174 (mtp) REVERT: B 249 LEU cc_start: 0.8187 (pp) cc_final: 0.7773 (tp) REVERT: B 254 LYS cc_start: 0.8510 (tptt) cc_final: 0.7814 (tppp) REVERT: D 249 LEU cc_start: 0.8130 (pp) cc_final: 0.7120 (mm) REVERT: D 270 MET cc_start: 0.5900 (mtt) cc_final: 0.5286 (tpt) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2796 time to fit residues: 124.2787 Evaluate side-chains 212 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 0.2980 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 145 optimal weight: 0.0570 chunk 105 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 168 optimal weight: 0.2980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A 810 ASN A 870 ASN A 892 ASN A 941 ASN ** A1338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN D 234 ASN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 18207 Z= 0.187 Angle : 0.677 14.368 24691 Z= 0.337 Chirality : 0.042 0.316 2910 Planarity : 0.006 0.129 3105 Dihedral : 5.351 84.734 2425 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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: -0.31 (0.19), residues: 2204 helix: 1.73 (0.15), residues: 1300 sheet: -1.74 (0.51), residues: 100 loop : -3.51 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A1950 HIS 0.005 0.001 HIS A1539 PHE 0.025 0.001 PHE A 69 TYR 0.014 0.001 TYR A1231 ARG 0.009 0.000 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ILE cc_start: 0.7925 (tp) cc_final: 0.7587 (mm) REVERT: A 384 MET cc_start: 0.8325 (tmm) cc_final: 0.8050 (tmm) REVERT: A 399 LEU cc_start: 0.9203 (tp) cc_final: 0.8876 (tt) REVERT: A 575 ILE cc_start: 0.9510 (mt) cc_final: 0.9205 (tt) REVERT: A 891 LEU cc_start: 0.9167 (tp) cc_final: 0.8386 (tt) REVERT: A 895 MET cc_start: 0.8398 (mmm) cc_final: 0.8118 (mmm) REVERT: A 973 MET cc_start: 0.5785 (mpp) cc_final: 0.5361 (mmt) REVERT: A 1520 MET cc_start: 0.8234 (mmm) cc_final: 0.7986 (tmm) REVERT: A 1646 LEU cc_start: 0.8085 (tt) cc_final: 0.7785 (mt) REVERT: A 1786 LYS cc_start: 0.9017 (tmtt) cc_final: 0.8388 (tptt) REVERT: A 1962 PHE cc_start: 0.8561 (t80) cc_final: 0.8162 (t80) REVERT: A 2034 GLU cc_start: 0.8607 (pt0) cc_final: 0.8339 (pt0) REVERT: F 362 LYS cc_start: 0.8732 (mttt) cc_final: 0.8427 (ttmm) REVERT: F 363 MET cc_start: 0.8538 (mmm) cc_final: 0.8293 (mmm) REVERT: F 382 ASP cc_start: 0.8499 (m-30) cc_final: 0.8248 (m-30) REVERT: F 387 ILE cc_start: 0.8853 (mm) cc_final: 0.8636 (mm) REVERT: B 249 LEU cc_start: 0.8307 (pp) cc_final: 0.7935 (tp) REVERT: B 254 LYS cc_start: 0.8439 (tptt) cc_final: 0.7791 (tppp) REVERT: D 249 LEU cc_start: 0.8246 (pp) cc_final: 0.7268 (mm) REVERT: D 270 MET cc_start: 0.5747 (mtt) cc_final: 0.5193 (tpt) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2812 time to fit residues: 128.9439 Evaluate side-chains 209 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 199 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 531 GLN A 684 ASN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 ASN A1209 ASN ** A1272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1929 ASN ** A2057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 18207 Z= 0.284 Angle : 0.745 13.933 24691 Z= 0.381 Chirality : 0.045 0.394 2910 Planarity : 0.007 0.169 3105 Dihedral : 5.771 88.902 2425 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.23 % Favored : 88.72 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: -0.55 (0.19), residues: 2204 helix: 1.48 (0.15), residues: 1303 sheet: -1.85 (0.50), residues: 101 loop : -3.53 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP A1950 HIS 0.008 0.001 HIS A1539 PHE 0.030 0.002 PHE A 69 TYR 0.018 0.002 TYR A1127 ARG 0.016 0.001 ARG E 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 2.151 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 98 ILE cc_start: 0.8245 (tp) cc_final: 0.7959 (mm) REVERT: A 399 LEU cc_start: 0.9233 (tp) cc_final: 0.8821 (tt) REVERT: A 575 ILE cc_start: 0.9559 (mt) cc_final: 0.9248 (tt) REVERT: A 891 LEU cc_start: 0.9219 (tp) cc_final: 0.8514 (tt) REVERT: A 895 MET cc_start: 0.8421 (mmm) cc_final: 0.8203 (mmm) REVERT: A 1520 MET cc_start: 0.8279 (mmm) cc_final: 0.7992 (tmm) REVERT: A 1646 LEU cc_start: 0.7975 (tt) cc_final: 0.7671 (mt) REVERT: F 362 LYS cc_start: 0.8779 (mttt) cc_final: 0.8520 (ttmm) REVERT: F 382 ASP cc_start: 0.8588 (m-30) cc_final: 0.8284 (m-30) REVERT: F 387 ILE cc_start: 0.8938 (mm) cc_final: 0.8710 (mm) REVERT: B 249 LEU cc_start: 0.8388 (pp) cc_final: 0.7960 (tp) REVERT: B 254 LYS cc_start: 0.8472 (tptt) cc_final: 0.7798 (tppp) REVERT: D 270 MET cc_start: 0.5725 (mtt) cc_final: 0.5421 (tmm) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.2828 time to fit residues: 121.6877 Evaluate side-chains 207 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 128 optimal weight: 0.0050 chunk 100 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 18 optimal weight: 0.0040 chunk 136 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 overall best weight: 0.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A 684 ASN A 849 ASN A 870 ASN A 941 ASN ** A1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1621 HIS ** A1772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1929 ASN ** A2057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18207 Z= 0.192 Angle : 0.696 11.467 24691 Z= 0.349 Chirality : 0.042 0.255 2910 Planarity : 0.005 0.104 3105 Dihedral : 5.541 88.147 2425 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -0.36 (0.19), residues: 2204 helix: 1.65 (0.15), residues: 1303 sheet: -1.83 (0.50), residues: 100 loop : -3.46 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A1950 HIS 0.005 0.001 HIS A 21 PHE 0.028 0.001 PHE A 69 TYR 0.014 0.001 TYR A1397 ARG 0.008 0.000 ARG C 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 2.186 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: A 98 ILE cc_start: 0.7978 (tp) cc_final: 0.7607 (mm) REVERT: A 399 LEU cc_start: 0.9218 (tp) cc_final: 0.8858 (tt) REVERT: A 575 ILE cc_start: 0.9532 (mt) cc_final: 0.9213 (tt) REVERT: A 891 LEU cc_start: 0.9140 (tp) cc_final: 0.8360 (tt) REVERT: A 895 MET cc_start: 0.8441 (mmm) cc_final: 0.8224 (mmm) REVERT: A 1520 MET cc_start: 0.8221 (mmm) cc_final: 0.7988 (tmm) REVERT: A 1646 LEU cc_start: 0.8111 (tt) cc_final: 0.7752 (mt) REVERT: A 2034 GLU cc_start: 0.8589 (pt0) cc_final: 0.8271 (pt0) REVERT: F 362 LYS cc_start: 0.8779 (mttt) cc_final: 0.8434 (ttmm) REVERT: F 363 MET cc_start: 0.8476 (mmm) cc_final: 0.8151 (mmm) REVERT: F 382 ASP cc_start: 0.8530 (m-30) cc_final: 0.8279 (m-30) REVERT: F 387 ILE cc_start: 0.8894 (mm) cc_final: 0.8678 (mm) REVERT: B 233 MET cc_start: 0.5324 (mtp) cc_final: 0.5029 (mtp) REVERT: B 249 LEU cc_start: 0.8379 (pp) cc_final: 0.8074 (tp) REVERT: B 254 LYS cc_start: 0.8411 (tptt) cc_final: 0.7720 (tppp) REVERT: C 245 SER cc_start: 0.8190 (m) cc_final: 0.7736 (t) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.2836 time to fit residues: 128.3665 Evaluate side-chains 210 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.5980 chunk 187 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 176 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN A 684 ASN ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 941 ASN ** A1076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2057 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.094361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.076265 restraints weight = 338023.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.080064 restraints weight = 172376.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.081147 restraints weight = 83776.772| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18207 Z= 0.235 Angle : 0.717 16.563 24691 Z= 0.362 Chirality : 0.043 0.303 2910 Planarity : 0.006 0.164 3105 Dihedral : 5.604 89.631 2425 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 2204 helix: 1.57 (0.15), residues: 1308 sheet: -1.81 (0.49), residues: 100 loop : -3.50 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A1950 HIS 0.006 0.001 HIS A1539 PHE 0.019 0.002 PHE A2052 TYR 0.014 0.001 TYR A 85 ARG 0.008 0.000 ARG C 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3708.78 seconds wall clock time: 68 minutes 43.41 seconds (4123.41 seconds total)