Starting phenix.real_space_refine on Mon Mar 18 19:27:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gln_40201/03_2024/8gln_40201_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gln_40201/03_2024/8gln_40201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gln_40201/03_2024/8gln_40201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gln_40201/03_2024/8gln_40201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gln_40201/03_2024/8gln_40201_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gln_40201/03_2024/8gln_40201_updated.pdb" } resolution = 2.2 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 13844 2.51 5 N 3668 2.21 5 O 4343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 136": "OD1" <-> "OD2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A ASP 889": "OD1" <-> "OD2" Residue "A GLU 900": "OE1" <-> "OE2" Residue "A ASP 928": "OD1" <-> "OD2" Residue "A PHE 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1258": "OD1" <-> "OD2" Residue "A ASP 1341": "OD1" <-> "OD2" Residue "A PHE 1346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1420": "OD1" <-> "OD2" Residue "A ASP 1424": "OD1" <-> "OD2" Residue "A GLU 1514": "OE1" <-> "OE2" Residue "A GLU 1559": "OE1" <-> "OE2" Residue "A GLU 1593": "OE1" <-> "OE2" Residue "A ASP 1645": "OD1" <-> "OD2" Residue "A PHE 1660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1746": "OE1" <-> "OE2" Residue "A ASP 1755": "OD1" <-> "OD2" Residue "A ASP 1812": "OD1" <-> "OD2" Residue "A GLU 1863": "OE1" <-> "OE2" Residue "A GLU 1990": "OE1" <-> "OE2" Residue "A ASP 2034": "OD1" <-> "OD2" Residue "A GLU 2039": "OE1" <-> "OE2" Residue "A ASP 2048": "OD1" <-> "OD2" Residue "A GLU 2053": "OE1" <-> "OE2" Residue "A TYR 2062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2081": "OE1" <-> "OE2" Residue "A ASP 2088": "OD1" <-> "OD2" Residue "A GLU 2103": "OE1" <-> "OE2" Residue "A TYR 2106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2247": "OE1" <-> "OE2" Residue "A PHE 2249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2272": "OD1" <-> "OD2" Residue "A TYR 2298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2340": "OD1" <-> "OD2" Residue "A TYR 2361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "F ASP 70": "OD1" <-> "OD2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F GLU 137": "OE1" <-> "OE2" Residue "F PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F ASP 334": "OD1" <-> "OD2" Residue "F TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 397": "OD1" <-> "OD2" Residue "F TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1061": "OE1" <-> "OE2" Residue "D PHE 1113": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21902 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2191, 17380 Classifications: {'peptide': 2191} Link IDs: {'PCIS': 3, 'PTRANS': 99, 'TRANS': 2088} Chain breaks: 3 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 2861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2861 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Chain: "D" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'TRANS': 74} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.08, per 1000 atoms: 0.51 Number of scatterers: 21902 At special positions: 0 Unit cell: (118.976, 129.792, 135.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 4343 8.00 N 3668 7.00 C 13844 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: 8.58 Conformation dependent library (CDL) restraints added in 3.9 seconds 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 29 sheets defined 11.2% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.69 Creating SS restraints... Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 296 through 306 removed outlier: 4.597A pdb=" N ASP A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 402 through 405 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 518 through 522 Processing helix chain 'A' and resid 579 through 582 No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 627 through 633 Processing helix chain 'A' and resid 644 through 646 No H-bonds generated for 'chain 'A' and resid 644 through 646' Processing helix chain 'A' and resid 651 through 654 No H-bonds generated for 'chain 'A' and resid 651 through 654' Processing helix chain 'A' and resid 658 through 661 No H-bonds generated for 'chain 'A' and resid 658 through 661' Processing helix chain 'A' and resid 664 through 669 removed outlier: 4.064A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 734 No H-bonds generated for 'chain 'A' and resid 731 through 734' Processing helix chain 'A' and resid 811 through 819 Processing helix chain 'A' and resid 846 through 848 No H-bonds generated for 'chain 'A' and resid 846 through 848' Processing helix chain 'A' and resid 873 through 875 No H-bonds generated for 'chain 'A' and resid 873 through 875' Processing helix chain 'A' and resid 899 through 902 Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.607A pdb=" N SER A 919 " --> pdb=" O VAL A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 943 No H-bonds generated for 'chain 'A' and resid 940 through 943' Processing helix chain 'A' and resid 983 through 985 No H-bonds generated for 'chain 'A' and resid 983 through 985' Processing helix chain 'A' and resid 999 through 1002 No H-bonds generated for 'chain 'A' and resid 999 through 1002' Processing helix chain 'A' and resid 1049 through 1051 No H-bonds generated for 'chain 'A' and resid 1049 through 1051' Processing helix chain 'A' and resid 1082 through 1088 Processing helix chain 'A' and resid 1100 through 1103 No H-bonds generated for 'chain 'A' and resid 1100 through 1103' Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1128 through 1132 Processing helix chain 'A' and resid 1413 through 1416 No H-bonds generated for 'chain 'A' and resid 1413 through 1416' Processing helix chain 'A' and resid 1419 through 1421 No H-bonds generated for 'chain 'A' and resid 1419 through 1421' Processing helix chain 'A' and resid 1427 through 1439 removed outlier: 4.118A pdb=" N SER A1439 " --> pdb=" O ILE A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1457 No H-bonds generated for 'chain 'A' and resid 1455 through 1457' Processing helix chain 'A' and resid 1572 through 1575 Processing helix chain 'A' and resid 1608 through 1613 Processing helix chain 'A' and resid 1618 through 1627 Processing helix chain 'A' and resid 1657 through 1659 No H-bonds generated for 'chain 'A' and resid 1657 through 1659' Processing helix chain 'A' and resid 1831 through 1833 No H-bonds generated for 'chain 'A' and resid 1831 through 1833' Processing helix chain 'A' and resid 1857 through 1860 No H-bonds generated for 'chain 'A' and resid 1857 through 1860' Processing helix chain 'A' and resid 1942 through 1944 No H-bonds generated for 'chain 'A' and resid 1942 through 1944' Processing helix chain 'A' and resid 1977 through 1980 No H-bonds generated for 'chain 'A' and resid 1977 through 1980' Processing helix chain 'A' and resid 1988 through 1993 Processing helix chain 'A' and resid 2072 through 2074 No H-bonds generated for 'chain 'A' and resid 2072 through 2074' Processing helix chain 'A' and resid 2085 through 2105 removed outlier: 3.681A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2135 Processing helix chain 'A' and resid 2148 through 2160 Proline residue: A2153 - end of helix Processing helix chain 'A' and resid 2187 through 2189 No H-bonds generated for 'chain 'A' and resid 2187 through 2189' Processing helix chain 'B' and resid 28 through 41 Processing helix chain 'B' and resid 127 through 135 Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'F' and resid 31 through 34 Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 62 through 67 removed outlier: 3.643A pdb=" N ALA F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 296 Processing helix chain 'F' and resid 300 through 307 removed outlier: 3.754A pdb=" N PHE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 321 removed outlier: 3.778A pdb=" N LYS F 320 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU F 321 " --> pdb=" O GLU F 317 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 138 through 140 removed outlier: 3.747A pdb=" N MET A 180 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE A 205 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN A 246 " --> pdb=" O GLN A 218 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL A 220 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS A 244 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 222 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY A 242 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN A 224 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 240 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG A 755 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 754 " --> pdb=" O ARG A 782 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN A 830 " --> pdb=" O ASN A1528 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN A1743 " --> pdb=" O ALA A1677 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR A1679 " --> pdb=" O ARG A1741 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG A1741 " --> pdb=" O TYR A1679 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP A1681 " --> pdb=" O SER A1739 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER A1739 " --> pdb=" O ASP A1681 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN A1683 " --> pdb=" O ARG A1737 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG A1737 " --> pdb=" O GLN A1683 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN A1685 " --> pdb=" O ILE A1735 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A1735 " --> pdb=" O ASN A1685 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA A1687 " --> pdb=" O THR A1733 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR A1733 " --> pdb=" O ALA A1687 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASN A1689 " --> pdb=" O PHE A1731 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N PHE A1731 " --> pdb=" O ASN A1689 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA A1691 " --> pdb=" O ILE A1729 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE A1729 " --> pdb=" O ALA A1691 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 166 through 173 removed outlier: 4.044A pdb=" N ASN A2351 " --> pdb=" O LYS A2379 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR A2334 " --> pdb=" O ALA A2347 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY A2349 " --> pdb=" O ASN A2332 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN A2332 " --> pdb=" O GLY A2349 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN A2351 " --> pdb=" O ARG A2330 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ARG A2330 " --> pdb=" O ASN A2351 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TRP A2353 " --> pdb=" O SER A2328 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER A2328 " --> pdb=" O TRP A2353 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU A2355 " --> pdb=" O ASP A2326 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP A2326 " --> pdb=" O LEU A2355 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU A2357 " --> pdb=" O LYS A2324 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS A2324 " --> pdb=" O LEU A2357 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA A2359 " --> pdb=" O ASN A2322 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASN A2322 " --> pdb=" O ALA A2359 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL A2287 " --> pdb=" O ALA A2274 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A2208 " --> pdb=" O THR A2069 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ASN A1874 " --> pdb=" O GLY A1962 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR A1847 " --> pdb=" O SER A1881 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN A1787 " --> pdb=" O ASN A1817 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HIS A1819 " --> pdb=" O THR A1785 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR A1785 " --> pdb=" O HIS A1819 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN A1821 " --> pdb=" O SER A1783 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER A1783 " --> pdb=" O GLN A1821 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A1823 " --> pdb=" O ASN A1781 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN A1781 " --> pdb=" O LEU A1823 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU A1825 " --> pdb=" O LYS A1779 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS A1779 " --> pdb=" O LEU A1825 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1780 " --> pdb=" O PHE A1772 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A1728 " --> pdb=" O GLY A1771 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 264 through 270 Processing sheet with id= D, first strand: chain 'A' and resid 275 through 282 Processing sheet with id= E, first strand: chain 'A' and resid 291 through 293 removed outlier: 3.884A pdb=" N TYR A 447 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 425 through 428 removed outlier: 5.980A pdb=" N LEU A 503 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU A 347 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 505 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 11.832A pdb=" N VAL A 504 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N PHE A 464 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A 460 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR A 467 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 465 through 468 Processing sheet with id= H, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= I, first strand: chain 'A' and resid 527 through 529 Processing sheet with id= J, first strand: chain 'A' and resid 717 through 720 Processing sheet with id= K, first strand: chain 'A' and resid 803 through 806 removed outlier: 3.541A pdb=" N SER A 767 " --> pdb=" O PHE A 770 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE A 772 " --> pdb=" O LYS A 765 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LYS A 765 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 866 through 869 removed outlier: 3.610A pdb=" N ASP A1194 " --> pdb=" O GLN A1215 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS A1217 " --> pdb=" O ILE A1192 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE A1192 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1250 through 1254 removed outlier: 3.518A pdb=" N LYS A 907 " --> pdb=" O TYR A 965 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 987 through 993 Processing sheet with id= O, first strand: chain 'A' and resid 1283 through 1291 Processing sheet with id= P, first strand: chain 'A' and resid 1313 through 1315 Processing sheet with id= Q, first strand: chain 'A' and resid 1342 through 1347 Processing sheet with id= R, first strand: chain 'A' and resid 1423 through 1426 removed outlier: 6.467A pdb=" N LEU A1510 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR A 857 " --> pdb=" O LEU A1510 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 1581 through 1583 removed outlier: 4.261A pdb=" N GLY A1581 " --> pdb=" O ASP A1645 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 1848 through 1853 Processing sheet with id= U, first strand: chain 'A' and resid 2264 through 2269 removed outlier: 3.647A pdb=" N ILE A2253 " --> pdb=" O ILE A2269 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A2199 " --> pdb=" O GLU A2258 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN A1947 " --> pdb=" O ASN A2020 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 2044 through 2047 Processing sheet with id= W, first strand: chain 'A' and resid 2215 through 2217 Processing sheet with id= X, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= Y, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.711A pdb=" N GLU B 141 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 90 through 98 removed outlier: 6.413A pdb=" N LEU F 387 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 118 through 120 removed outlier: 4.161A pdb=" N ARG F 131 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 1041 through 1045 removed outlier: 3.633A pdb=" N ILE D1050 " --> pdb=" O VAL D1085 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 1106 through 1113 removed outlier: 4.277A pdb=" N GLN D1093 " --> pdb=" O PHE D1113 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP D1066 " --> pdb=" O LEU D1071 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU D1071 " --> pdb=" O ASP D1066 " (cutoff:3.500A) 804 hydrogen bonds defined for protein. 2196 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: 12.93 Time building geometry restraints manager: 9.36 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: 7258 1.34 - 1.46: 5215 1.46 - 1.58: 9810 1.58 - 1.70: 5 1.70 - 1.82: 92 Bond restraints: 22380 Sorted by residual: bond pdb=" C1 LMN A2501 " pdb=" O5 LMN A2501 " ideal model delta sigma weight residual 1.403 1.565 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" C4 LMN A2501 " pdb=" O4 LMN A2501 " ideal model delta sigma weight residual 1.409 1.506 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" CCF LMN A2501 " pdb=" OBX LMN A2501 " ideal model delta sigma weight residual 1.410 1.501 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" CCS LMN A2501 " pdb=" OBZ LMN A2501 " ideal model delta sigma weight residual 1.394 1.482 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CCR LMN A2501 " pdb=" OBY LMN A2501 " ideal model delta sigma weight residual 1.393 1.476 -0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 22375 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.95: 516 106.95 - 113.73: 12001 113.73 - 120.50: 8501 120.50 - 127.27: 9238 127.27 - 134.05: 124 Bond angle restraints: 30380 Sorted by residual: angle pdb=" C4 LMN A2501 " pdb=" O4 LMN A2501 " pdb=" CCR LMN A2501 " ideal model delta sigma weight residual 120.22 109.78 10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C GLN A 538 " pdb=" N ASP A 539 " pdb=" CA ASP A 539 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 angle pdb=" CCQ LMN A2501 " pdb=" OCB LMN A2501 " pdb=" CCS LMN A2501 " ideal model delta sigma weight residual 119.65 110.13 9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C ILE B 100 " pdb=" CA ILE B 100 " pdb=" CB ILE B 100 " ideal model delta sigma weight residual 111.29 116.49 -5.20 1.64e+00 3.72e-01 1.01e+01 angle pdb=" C SER A2050 " pdb=" N THR A2051 " pdb=" CA THR A2051 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.58e+00 ... (remaining 30375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.78: 12444 24.78 - 49.56: 785 49.56 - 74.34: 115 74.34 - 99.12: 53 99.12 - 123.90: 16 Dihedral angle restraints: 13413 sinusoidal: 5391 harmonic: 8022 Sorted by residual: dihedral pdb=" CA PRO A1063 " pdb=" C PRO A1063 " pdb=" N LEU A1064 " pdb=" CA LEU A1064 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASP A1258 " pdb=" C ASP A1258 " pdb=" N LEU A1259 " pdb=" CA LEU A1259 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA PHE A1078 " pdb=" C PHE A1078 " pdb=" N ASP A1079 " pdb=" CA ASP A1079 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 13410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2158 0.035 - 0.071: 735 0.071 - 0.106: 288 0.106 - 0.141: 119 0.141 - 0.177: 7 Chirality restraints: 3307 Sorted by residual: chirality pdb=" CA ASP A1281 " pdb=" N ASP A1281 " pdb=" C ASP A1281 " pdb=" CB ASP A1281 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CB ILE B 100 " pdb=" CA ILE B 100 " pdb=" CG1 ILE B 100 " pdb=" CG2 ILE B 100 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CCV LMN A2501 " pdb=" CCR LMN A2501 " pdb=" CCT LMN A2501 " pdb=" OAU LMN A2501 " both_signs ideal model delta sigma weight residual False 2.28 2.45 -0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 3304 not shown) Planarity restraints: 4022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1651 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A1652 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A1652 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1652 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 125 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO F 126 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO F 126 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 126 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 133 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO B 134 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 134 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 134 " 0.025 5.00e-02 4.00e+02 ... (remaining 4019 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 289 2.65 - 3.21: 19402 3.21 - 3.77: 35096 3.77 - 4.34: 51095 4.34 - 4.90: 82611 Nonbonded interactions: 188493 Sorted by model distance: nonbonded pdb=" ND2 ASN A 343 " pdb=" O GLU A 429 " model vdw 2.084 2.520 nonbonded pdb=" OE2 GLU B 32 " pdb=" OH TYR B 54 " model vdw 2.154 2.440 nonbonded pdb=" OG SER F 75 " pdb=" OG1 THR F 95 " model vdw 2.155 2.440 nonbonded pdb=" ND2 ASN A1392 " pdb=" O GLY A1476 " model vdw 2.161 2.520 nonbonded pdb=" OH TYR A2115 " pdb=" O ILE A2141 " model vdw 2.169 2.440 ... (remaining 188488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.980 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: 0.000 Extract box with map and model: 13.120 Check model and map are aligned: 0.000 Set scattering table: 0.050 Process input model: 63.800 Find NCS groups from input model: 0.570 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:13.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 0.162 22380 Z= 0.228 Angle : 0.585 10.435 30380 Z= 0.304 Chirality : 0.045 0.177 3307 Planarity : 0.004 0.053 4022 Dihedral : 17.394 123.900 8293 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.19 % Favored : 95.77 % Rotamer: Outliers : 1.04 % Allowed : 10.94 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: 0.11 (0.16), residues: 2743 helix: -0.51 (0.30), residues: 291 sheet: 0.82 (0.16), residues: 1061 loop : -0.33 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1996 HIS 0.005 0.001 HIS A 291 PHE 0.015 0.001 PHE A1480 TYR 0.020 0.001 TYR A 534 ARG 0.010 0.000 ARG A2264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 259 time to evaluate : 2.445 Fit side-chains revert: symmetry clash REVERT: A 2400 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8144 (m110) REVERT: D 1053 ASN cc_start: 0.7407 (m110) cc_final: 0.7102 (m-40) outliers start: 25 outliers final: 10 residues processed: 282 average time/residue: 1.2679 time to fit residues: 411.0676 Evaluate side-chains 217 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 206 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 1878 ASN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 392 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 10.0000 chunk 207 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 ASN A 418 ASN A 437 ASN A 581 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1316 ASN ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 ASN A1485 ASN ** A1650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1695 GLN A1740 ASN A1955 ASN A2040 ASN A2136 ASN B 155 ASN D1089 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 22380 Z= 0.467 Angle : 0.688 9.247 30380 Z= 0.362 Chirality : 0.051 0.327 3307 Planarity : 0.005 0.051 4022 Dihedral : 9.888 105.629 3161 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.32 % Favored : 94.64 % Rotamer: Outliers : 3.00 % Allowed : 11.53 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.07 (0.16), residues: 2743 helix: -0.59 (0.31), residues: 286 sheet: 0.67 (0.16), residues: 1049 loop : -0.42 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1996 HIS 0.005 0.001 HIS A 291 PHE 0.025 0.002 PHE A1009 TYR 0.021 0.002 TYR A1104 ARG 0.007 0.001 ARG A2264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 212 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 747 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7990 (p0) REVERT: A 2400 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8034 (m110) outliers start: 72 outliers final: 39 residues processed: 261 average time/residue: 1.2666 time to fit residues: 380.2738 Evaluate side-chains 247 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2026 ASP Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2201 SER Chi-restraints excluded: chain A residue 2332 ASN Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 249 optimal weight: 5.9990 chunk 269 optimal weight: 0.9980 chunk 221 optimal weight: 0.0970 chunk 247 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 437 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN A1222 GLN A1316 ASN ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1387 ASN A1650 GLN A1695 GLN A1740 ASN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN D1053 ASN D1089 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22380 Z= 0.324 Angle : 0.622 8.714 30380 Z= 0.326 Chirality : 0.048 0.316 3307 Planarity : 0.004 0.046 4022 Dihedral : 8.991 98.114 3155 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 2.91 % Allowed : 11.99 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.17 (0.16), residues: 2743 helix: -0.63 (0.31), residues: 292 sheet: 0.57 (0.16), residues: 1054 loop : -0.46 (0.17), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1580 HIS 0.004 0.001 HIS A 291 PHE 0.023 0.002 PHE A1009 TYR 0.016 0.001 TYR A1104 ARG 0.007 0.000 ARG A2264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 213 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 747 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7977 (p0) REVERT: A 779 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7014 (tmm) REVERT: A 2400 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.8079 (m110) REVERT: F 199 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7534 (p0) outliers start: 70 outliers final: 38 residues processed: 269 average time/residue: 1.3720 time to fit residues: 424.2155 Evaluate side-chains 245 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 203 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2201 SER Chi-restraints excluded: chain A residue 2207 ARG Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2332 ASN Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 246 optimal weight: 5.9990 chunk 187 optimal weight: 0.0040 chunk 129 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 264 optimal weight: 3.9990 chunk 130 optimal weight: 0.0980 chunk 237 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 437 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1695 GLN A1740 ASN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 155 ASN D1089 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22380 Z= 0.304 Angle : 0.612 10.179 30380 Z= 0.320 Chirality : 0.048 0.335 3307 Planarity : 0.004 0.047 4022 Dihedral : 8.441 87.484 3153 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.83 % Allowed : 13.11 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.20 (0.16), residues: 2743 helix: -0.62 (0.31), residues: 292 sheet: 0.53 (0.16), residues: 1055 loop : -0.48 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1580 HIS 0.003 0.001 HIS A 291 PHE 0.023 0.001 PHE A1009 TYR 0.017 0.001 TYR B 55 ARG 0.008 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 209 time to evaluate : 2.351 Fit side-chains revert: symmetry clash REVERT: A 2400 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7949 (m110) REVERT: F 199 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7502 (p0) outliers start: 68 outliers final: 42 residues processed: 259 average time/residue: 1.4089 time to fit residues: 418.9016 Evaluate side-chains 244 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 200 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1849 ASP Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2026 ASP Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2207 ARG Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 220 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 226 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN A 613 GLN A1222 GLN ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 GLN A1695 GLN A1740 ASN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 149 HIS B 155 ASN D1089 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22380 Z= 0.235 Angle : 0.589 10.045 30380 Z= 0.307 Chirality : 0.047 0.355 3307 Planarity : 0.004 0.069 4022 Dihedral : 7.816 85.272 3153 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.87 % Allowed : 13.19 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.20 (0.16), residues: 2743 helix: -0.57 (0.31), residues: 291 sheet: 0.53 (0.16), residues: 1053 loop : -0.49 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1580 HIS 0.003 0.001 HIS A 291 PHE 0.022 0.001 PHE A1009 TYR 0.018 0.001 TYR B 55 ARG 0.014 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 212 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.7510 (mmm-85) cc_final: 0.7278 (mtp180) REVERT: A 846 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8209 (mptp) REVERT: A 884 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.6970 (tp) REVERT: F 199 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7441 (p0) outliers start: 69 outliers final: 35 residues processed: 266 average time/residue: 1.3149 time to fit residues: 403.4837 Evaluate side-chains 245 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 207 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 846 LYS Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2026 ASP Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 89 optimal weight: 8.9990 chunk 238 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 265 optimal weight: 7.9990 chunk 220 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 437 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 ASN A1123 ASN ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1583 ASN A1650 GLN A1695 GLN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN B 143 GLN B 155 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 22380 Z= 0.458 Angle : 0.663 10.858 30380 Z= 0.348 Chirality : 0.050 0.355 3307 Planarity : 0.005 0.046 4022 Dihedral : 7.665 85.170 3151 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.70 % Allowed : 13.77 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.29 (0.16), residues: 2743 helix: -0.81 (0.30), residues: 298 sheet: 0.50 (0.16), residues: 1047 loop : -0.54 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1580 HIS 0.005 0.001 HIS A1672 PHE 0.024 0.002 PHE A1009 TYR 0.020 0.002 TYR A1104 ARG 0.011 0.001 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 210 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 779 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7027 (tmm) REVERT: A 846 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8249 (mptp) REVERT: A 2400 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.8006 (m110) REVERT: F 199 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7648 (p0) outliers start: 65 outliers final: 34 residues processed: 256 average time/residue: 1.3365 time to fit residues: 393.2158 Evaluate side-chains 241 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 203 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 846 LYS Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2026 ASP Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2201 SER Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 255 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 223 optimal weight: 8.9990 chunk 148 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1695 GLN A1740 ASN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 155 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22380 Z= 0.246 Angle : 0.600 10.017 30380 Z= 0.313 Chirality : 0.047 0.370 3307 Planarity : 0.004 0.045 4022 Dihedral : 7.060 84.817 3149 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.29 % Allowed : 14.61 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.25 (0.16), residues: 2743 helix: -0.70 (0.31), residues: 298 sheet: 0.52 (0.16), residues: 1048 loop : -0.51 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1580 HIS 0.003 0.001 HIS A1672 PHE 0.023 0.001 PHE A1009 TYR 0.021 0.001 TYR B 55 ARG 0.009 0.000 ARG A2199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 213 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 846 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8218 (mptp) REVERT: A 1592 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6823 (pt0) outliers start: 55 outliers final: 36 residues processed: 254 average time/residue: 1.3912 time to fit residues: 404.2387 Evaluate side-chains 248 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 210 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 846 LYS Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1243 MET Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1592 GLU Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2026 ASP Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2201 SER Chi-restraints excluded: chain A residue 2255 MET Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 79 optimal weight: 0.0370 chunk 51 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 437 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 GLN A1695 GLN A1740 ASN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 155 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22380 Z= 0.300 Angle : 0.613 10.311 30380 Z= 0.320 Chirality : 0.048 0.363 3307 Planarity : 0.004 0.044 4022 Dihedral : 6.912 84.206 3149 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.29 % Allowed : 14.65 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.28 (0.16), residues: 2743 helix: -0.74 (0.31), residues: 299 sheet: 0.48 (0.16), residues: 1051 loop : -0.51 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1580 HIS 0.004 0.001 HIS A1672 PHE 0.023 0.001 PHE A1009 TYR 0.022 0.001 TYR B 55 ARG 0.008 0.000 ARG A2199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 211 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 846 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8204 (mptp) REVERT: A 862 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.4886 (mp0) REVERT: A 1592 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6853 (pt0) outliers start: 55 outliers final: 37 residues processed: 251 average time/residue: 1.3560 time to fit residues: 392.0297 Evaluate side-chains 247 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 207 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 846 LYS Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1243 MET Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1592 GLU Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2026 ASP Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2201 SER Chi-restraints excluded: chain A residue 2255 MET Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 253 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 245 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1695 GLN A1740 ASN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 155 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22380 Z= 0.212 Angle : 0.586 8.725 30380 Z= 0.305 Chirality : 0.046 0.325 3307 Planarity : 0.004 0.043 4022 Dihedral : 6.568 83.628 3149 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.96 % Allowed : 14.94 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.24 (0.16), residues: 2743 helix: -0.60 (0.31), residues: 292 sheet: 0.48 (0.16), residues: 1060 loop : -0.48 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1580 HIS 0.003 0.001 HIS A1672 PHE 0.022 0.001 PHE A1009 TYR 0.019 0.001 TYR B 55 ARG 0.008 0.000 ARG A2199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 216 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 846 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8193 (mptp) REVERT: A 884 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6820 (tp) outliers start: 47 outliers final: 30 residues processed: 252 average time/residue: 1.3859 time to fit residues: 402.2226 Evaluate side-chains 243 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 211 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 846 LYS Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2201 SER Chi-restraints excluded: chain A residue 2255 MET Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 161 optimal weight: 2.9990 chunk 260 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 167 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 GLN ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 GLN A1695 GLN A1740 ASN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 155 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 22380 Z= 0.422 Angle : 0.659 10.226 30380 Z= 0.345 Chirality : 0.049 0.320 3307 Planarity : 0.004 0.054 4022 Dihedral : 6.816 83.230 3148 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.14 % Favored : 94.82 % Rotamer: Outliers : 1.87 % Allowed : 15.06 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.29 (0.16), residues: 2743 helix: -0.70 (0.31), residues: 293 sheet: 0.45 (0.16), residues: 1057 loop : -0.51 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1580 HIS 0.005 0.001 HIS A1672 PHE 0.024 0.002 PHE A1009 TYR 0.022 0.002 TYR B 55 ARG 0.012 0.001 ARG A 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 207 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 846 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8239 (mptp) REVERT: A 862 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.4884 (mp0) outliers start: 45 outliers final: 32 residues processed: 242 average time/residue: 1.3519 time to fit residues: 375.8687 Evaluate side-chains 237 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 203 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 846 LYS Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1880 ASN Chi-restraints excluded: chain A residue 1956 SER Chi-restraints excluded: chain A residue 2008 THR Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2201 SER Chi-restraints excluded: chain A residue 2255 MET Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 401 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 172 optimal weight: 0.6980 chunk 231 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 217 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 437 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1695 GLN A1740 ASN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 155 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.095345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.073525 restraints weight = 35222.457| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.21 r_work: 0.2879 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22380 Z= 0.192 Angle : 0.588 9.074 30380 Z= 0.307 Chirality : 0.046 0.278 3307 Planarity : 0.004 0.084 4022 Dihedral : 6.470 82.946 3148 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.41 % Allowed : 15.69 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.25 (0.16), residues: 2743 helix: -0.62 (0.31), residues: 292 sheet: 0.45 (0.16), residues: 1058 loop : -0.48 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1580 HIS 0.003 0.001 HIS A1672 PHE 0.022 0.001 PHE A1009 TYR 0.021 0.001 TYR B 55 ARG 0.019 0.000 ARG A 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7920.88 seconds wall clock time: 141 minutes 30.84 seconds (8490.84 seconds total)