Starting phenix.real_space_refine on Tue Jul 23 12:56:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gln_40201/07_2024/8gln_40201.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gln_40201/07_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_40201/07_2024/8gln_40201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gln_40201/07_2024/8gln_40201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gln_40201/07_2024/8gln_40201.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gln_40201/07_2024/8gln_40201.cif" } 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-5388/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: 11.86, per 1000 atoms: 0.54 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: 8.25 Conformation dependent library (CDL) restraints added in 3.8 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... Secondary structure from input PDB file: 59 helices and 23 sheets defined 14.6% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 295 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 359 through 363 Processing helix chain 'A' and resid 382 through 386 removed outlier: 4.025A pdb=" N ASN A 386 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.579A pdb=" N ILE A 393 " --> pdb=" O PRO A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 517 through 523 removed outlier: 3.746A pdb=" N ASN A 521 " --> pdb=" O ASN A 517 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.970A pdb=" N LYS A 573 " --> pdb=" O PRO A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 626 through 634 Processing helix chain 'A' and resid 643 through 647 Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 730 through 735 removed outlier: 3.578A pdb=" N ALA A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 819 removed outlier: 3.802A pdb=" N THR A 814 " --> pdb=" O VAL A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 847 No H-bonds generated for 'chain 'A' and resid 845 through 847' Processing helix chain 'A' and resid 872 through 876 Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 940 through 944 Processing helix chain 'A' and resid 982 through 985 Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1048 through 1052 Processing helix chain 'A' and resid 1081 through 1089 Processing helix chain 'A' and resid 1099 through 1104 removed outlier: 4.102A pdb=" N ILE A1103 " --> pdb=" O ARG A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1108 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1412 through 1417 Processing helix chain 'A' and resid 1418 through 1422 Processing helix chain 'A' and resid 1427 through 1438 Processing helix chain 'A' and resid 1454 through 1458 Processing helix chain 'A' and resid 1573 through 1576 Processing helix chain 'A' and resid 1607 through 1614 Processing helix chain 'A' and resid 1617 through 1628 removed outlier: 3.608A pdb=" N ALA A1628 " --> pdb=" O ILE A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1658 No H-bonds generated for 'chain 'A' and resid 1656 through 1658' Processing helix chain 'A' and resid 1830 through 1834 removed outlier: 3.786A pdb=" N LYS A1833 " --> pdb=" O PRO A1830 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A1834 " --> pdb=" O ILE A1831 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1830 through 1834' Processing helix chain 'A' and resid 1856 through 1861 Processing helix chain 'A' and resid 1941 through 1943 No H-bonds generated for 'chain 'A' and resid 1941 through 1943' Processing helix chain 'A' and resid 1976 through 1981 Processing helix chain 'A' and resid 1987 through 1994 Processing helix chain 'A' and resid 2071 through 2075 Processing helix chain 'A' and resid 2084 through 2106 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 2129 through 2136 removed outlier: 3.513A pdb=" N ASN A2136 " --> pdb=" O VAL A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2147 through 2161 Proline residue: A2153 - end of helix Processing helix chain 'A' and resid 2186 through 2190 removed outlier: 3.560A pdb=" N ARG A2189 " --> pdb=" O GLY A2186 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A2190 " --> pdb=" O LEU A2187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2186 through 2190' Processing helix chain 'B' and resid 27 through 42 Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 38 through 44 Processing helix chain 'F' and resid 61 through 68 removed outlier: 3.643A pdb=" N ALA F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.756A pdb=" N ASP F 288 " --> pdb=" O GLN F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 308 removed outlier: 3.754A pdb=" N PHE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE F 308 " --> pdb=" O ILE F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 319 Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 140 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 138 through 140 current: chain 'A' and resid 166 through 173 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 173 current: chain 'A' and resid 187 through 194 removed outlier: 6.304A pdb=" N PHE A 205 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE A 217 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN A 248 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 219 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N MET A 227 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLN A 238 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR A 253 " --> pdb=" O GLU A 763 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG A 755 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE A 770 " --> pdb=" O ILE A 766 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 770 through 773 current: chain 'A' and resid 798 through 809 removed outlier: 3.850A pdb=" N ASN A 830 " --> pdb=" O ASN A1528 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1757 through 1760 current: chain 'A' and resid 1779 through 1789 removed outlier: 5.608A pdb=" N ILE A1789 " --> pdb=" O PRO A1816 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR A1847 " --> pdb=" O SER A1881 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A1876 " --> pdb=" O PRO A1961 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASN A1878 " --> pdb=" O VAL A1959 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL A1959 " --> pdb=" O ASN A1878 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASN A1880 " --> pdb=" O GLY A1957 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLY A1957 " --> pdb=" O ASN A1880 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN A1882 " --> pdb=" O ASN A1955 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASN A1955 " --> pdb=" O ASN A1882 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU A1884 " --> pdb=" O THR A1953 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N THR A1953 " --> pdb=" O LEU A1884 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR A1886 " --> pdb=" O ASN A1951 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASN A1951 " --> pdb=" O THR A1886 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2007 through 2015 current: chain 'A' and resid 2027 through 2032 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2027 through 2032 current: chain 'A' and resid 2054 through 2069 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2054 through 2069 current: chain 'A' and resid 2197 through 2217 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2238 through 2240 current: chain 'A' and resid 2264 through 2278 removed outlier: 4.030A pdb=" N VAL A2287 " --> pdb=" O ALA A2274 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP A2302 " --> pdb=" O SER A2319 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N SER A2319 " --> pdb=" O ASP A2302 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A2336 " --> pdb=" O LEU A2346 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU A2346 " --> pdb=" O VAL A2336 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN A2351 " --> pdb=" O LYS A2379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 270 Processing sheet with id=AA3, first strand: chain 'A' and resid 275 through 282 Processing sheet with id=AA4, 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=AA5, first strand: chain 'A' and resid 471 through 474 removed outlier: 6.203A pdb=" N LEU A 460 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N PHE A 464 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 11.832A pdb=" N VAL A 504 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 19.582A pdb=" N TYR A 466 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 23.885A pdb=" N SER A 502 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ARG A 342 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN A 430 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR A 467 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AA7, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA8, first strand: chain 'A' and resid 690 through 691 Processing sheet with id=AA9, first strand: chain 'A' and resid 849 through 850 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 853 through 859 current: chain 'A' and resid 1326 through 1337 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1326 through 1337 current: chain 'A' and resid 1423 through 1426 Processing sheet with id=AB1, first strand: chain 'A' and resid 866 through 869 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 866 through 869 current: chain 'A' and resid 960 through 969 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 960 through 969 current: chain 'A' and resid 1208 through 1219 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 877 through 878 Processing sheet with id=AB3, first strand: chain 'A' and resid 938 through 939 removed outlier: 4.606A pdb=" N ILE A 938 " --> pdb=" O VAL A 957 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1265 through 1266 Processing sheet with id=AB5, first strand: chain 'A' and resid 1313 through 1315 Processing sheet with id=AB6, 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=AB7, first strand: chain 'A' and resid 1862 through 1863 Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 48 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 54 through 59 current: chain 'B' and resid 110 through 113 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 110 through 113 current: chain 'B' and resid 167 through 174 Processing sheet with id=AB9, first strand: chain 'B' and resid 156 through 157 Processing sheet with id=AC1, first strand: chain 'F' and resid 193 through 194 removed outlier: 3.685A pdb=" N ASN F 199 " --> pdb=" O ILE F 240 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE F 240 " --> pdb=" O ASN F 199 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU F 387 " --> pdb=" O PRO F 80 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP F 397 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ASP F 70 " --> pdb=" O ASP F 397 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL F 182 " --> pdb=" O ASN F 210 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN F 210 " --> pdb=" O VAL F 182 " (cutoff:3.500A) Processing sheet with id=AC2, 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=AC3, first strand: chain 'F' and resid 215 through 220 removed outlier: 4.484A pdb=" N TYR F 217 " --> pdb=" O SER F 223 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N SER F 223 " --> pdb=" O TYR F 217 " (cutoff:3.500A) Processing sheet with id=AC4, 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=AC5, first strand: chain 'D' and resid 1071 through 1075 removed outlier: 5.933A pdb=" N LEU D1071 " --> pdb=" O ASP D1066 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP D1066 " --> pdb=" O LEU D1071 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN D1093 " --> pdb=" O PHE D1113 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 1920 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: 12.27 Time building geometry restraints manager: 9.19 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: 293 2.65 - 3.21: 19477 3.21 - 3.77: 35211 3.77 - 4.34: 51199 4.34 - 4.90: 82613 Nonbonded interactions: 188793 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 188788 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 61.850 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.020 ------------------------------------------------------------------------------- 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= 0.221 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 : 2.400 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: 1.2778 time to fit residues: 414.1886 Evaluate side-chains 217 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 206 time to evaluate : 2.425 ------------------------------------------------------------------------------- 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: 1.9990 chunk 115 optimal weight: 0.4980 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: 2.9990 chunk 130 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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** A1222 GLN 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 A2136 ASN B 155 ASN D1089 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 22380 Z= 0.419 Angle : 0.665 8.860 30380 Z= 0.349 Chirality : 0.050 0.323 3307 Planarity : 0.005 0.050 4022 Dihedral : 9.826 105.800 3161 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.96 % Favored : 95.01 % Rotamer: Outliers : 2.95 % Allowed : 11.69 % Favored : 85.35 % 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: -0.08 (0.16), residues: 2743 helix: -0.64 (0.30), residues: 294 sheet: 0.67 (0.16), residues: 1048 loop : -0.42 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1996 HIS 0.005 0.001 HIS A 291 PHE 0.024 0.002 PHE A1480 TYR 0.019 0.002 TYR A2159 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: 71 poor density : 213 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 747 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7953 (p0) REVERT: A 779 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7037 (tmm) REVERT: A 884 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7090 (tp) REVERT: A 2400 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8025 (m110) outliers start: 71 outliers final: 36 residues processed: 262 average time/residue: 1.3059 time to fit residues: 392.2955 Evaluate side-chains 242 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 202 time to evaluate : 2.573 ------------------------------------------------------------------------------- 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 779 MET 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 1878 ASN Chi-restraints excluded: chain A residue 1956 SER 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 2247 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 93 LEU Chi-restraints excluded: chain B residue 95 SER 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: 0.9990 chunk 77 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 269 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 199 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 437 ASN A 581 ASN A1316 ASN ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 GLN A1695 GLN A1740 ASN B 143 GLN B 155 ASN D1053 ASN D1089 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22380 Z= 0.209 Angle : 0.578 8.772 30380 Z= 0.300 Chirality : 0.047 0.312 3307 Planarity : 0.004 0.044 4022 Dihedral : 8.926 101.372 3157 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.12 % Favored : 95.84 % Rotamer: Outliers : 2.54 % Allowed : 12.28 % Favored : 85.19 % 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: -0.09 (0.16), residues: 2743 helix: -0.52 (0.31), residues: 286 sheet: 0.59 (0.16), residues: 1059 loop : -0.40 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1996 HIS 0.003 0.001 HIS A 291 PHE 0.015 0.001 PHE A1480 TYR 0.014 0.001 TYR A2159 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 278 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 217 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2400 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.8037 (m110) REVERT: B 32 GLU cc_start: 0.8053 (tp30) cc_final: 0.7825 (tp30) outliers start: 61 outliers final: 27 residues processed: 264 average time/residue: 1.2996 time to fit residues: 395.4130 Evaluate side-chains 237 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 209 time to evaluate : 2.490 ------------------------------------------------------------------------------- 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 699 GLN 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 1179 ILE Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1878 ASN Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2332 ASN 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 58 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 SER 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 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: 10.0000 chunk 187 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 250 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 581 ASN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1316 ASN ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1387 ASN A1695 GLN A1740 ASN B 96 ASN B 155 ASN D1089 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.006 0.059 22380 Z= 0.401 Angle : 0.642 10.006 30380 Z= 0.336 Chirality : 0.049 0.323 3307 Planarity : 0.004 0.043 4022 Dihedral : 8.654 89.695 3155 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.91 % Allowed : 12.65 % Favored : 84.44 % 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: -0.76 (0.30), residues: 299 sheet: 0.52 (0.16), residues: 1055 loop : -0.49 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1580 HIS 0.004 0.001 HIS F 219 PHE 0.024 0.002 PHE A1480 TYR 0.019 0.002 TYR A2159 ARG 0.008 0.001 ARG A 235 *********************** 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 275 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 205 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 779 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6999 (tmm) REVERT: A 2400 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7929 (m110) REVERT: F 199 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7546 (p0) outliers start: 70 outliers final: 40 residues processed: 257 average time/residue: 1.2826 time to fit residues: 380.2289 Evaluate side-chains 242 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 199 time to evaluate : 2.574 ------------------------------------------------------------------------------- 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 768 ASP 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 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 1878 ASN Chi-restraints excluded: chain A residue 1956 SER 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 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 58 THR 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 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 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: 0.9990 chunk 150 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 197 optimal weight: 0.0370 chunk 109 optimal weight: 0.8980 chunk 226 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 581 ASN 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** A1583 ASN A1650 GLN A1695 GLN A1740 ASN B 143 GLN B 149 HIS B 155 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22380 Z= 0.165 Angle : 0.565 9.684 30380 Z= 0.293 Chirality : 0.046 0.344 3307 Planarity : 0.004 0.044 4022 Dihedral : 7.780 85.332 3155 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.96 % Allowed : 13.94 % Favored : 84.10 % 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: -0.19 (0.16), residues: 2743 helix: -0.65 (0.31), residues: 291 sheet: 0.51 (0.16), residues: 1061 loop : -0.44 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1580 HIS 0.003 0.001 HIS A 291 PHE 0.014 0.001 PHE A1242 TYR 0.011 0.001 TYR A2159 ARG 0.007 0.000 ARG A1643 *********************** 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 262 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 215 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 884 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6830 (tp) REVERT: B 32 GLU cc_start: 0.8160 (tp30) cc_final: 0.7945 (tp30) outliers start: 47 outliers final: 28 residues processed: 251 average time/residue: 1.3195 time to fit residues: 381.0793 Evaluate side-chains 238 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 780 THR 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 2030 ASP Chi-restraints excluded: chain A residue 2106 TYR Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2201 SER Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2332 ASN Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 SER 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=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: 1.9990 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 265 optimal weight: 0.0060 chunk 220 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- 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 ** 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 A2331 ASN B 96 ASN B 143 GLN B 155 ASN D1074 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1441 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= 0.271 Angle : 0.589 10.106 30380 Z= 0.307 Chirality : 0.047 0.358 3307 Planarity : 0.004 0.044 4022 Dihedral : 7.208 84.489 3149 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.29 % Allowed : 13.86 % Favored : 83.85 % 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: -0.21 (0.16), residues: 2743 helix: -0.70 (0.30), residues: 299 sheet: 0.52 (0.16), residues: 1055 loop : -0.46 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1580 HIS 0.003 0.001 HIS A 291 PHE 0.021 0.001 PHE A1480 TYR 0.015 0.001 TYR A2159 ARG 0.011 0.000 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 265 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 210 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 884 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.6895 (tp) REVERT: A 2273 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7612 (mtm180) outliers start: 55 outliers final: 36 residues processed: 250 average time/residue: 1.3686 time to fit residues: 392.1945 Evaluate side-chains 242 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 2.656 ------------------------------------------------------------------------------- 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 699 GLN 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 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 2026 ASP Chi-restraints excluded: chain A residue 2106 TYR 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 2247 GLU Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2273 ARG 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 B residue 42 ASN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 58 THR 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 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 1054 SER Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 255 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 165 optimal weight: 0.0870 chunk 161 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- 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 581 ASN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 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 B 96 ASN B 143 GLN B 155 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1533 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= 0.401 Angle : 0.647 11.000 30380 Z= 0.338 Chirality : 0.049 0.368 3307 Planarity : 0.004 0.044 4022 Dihedral : 7.157 84.283 3149 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.58 % Allowed : 14.02 % Favored : 83.40 % 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: -0.32 (0.16), residues: 2743 helix: -0.78 (0.30), residues: 301 sheet: 0.39 (0.16), residues: 1065 loop : -0.48 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1580 HIS 0.005 0.001 HIS A1672 PHE 0.023 0.002 PHE A1480 TYR 0.019 0.002 TYR A1104 ARG 0.010 0.001 ARG A 331 *********************** 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 267 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 205 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 846 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8242 (mptp) outliers start: 62 outliers final: 42 residues processed: 252 average time/residue: 1.3829 time to fit residues: 407.0791 Evaluate side-chains 247 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 204 time to evaluate : 2.221 ------------------------------------------------------------------------------- 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 747 ASN Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 772 ILE 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 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 2207 ARG Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2268 GLU Chi-restraints excluded: chain A residue 2273 ARG Chi-restraints excluded: chain A residue 2332 ASN 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 58 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 0.0370 chunk 167 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 overall best weight: 0.9264 ------------------------------------------------------------------------------- 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 581 ASN ** 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** ** 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: 0.8283 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22380 Z= 0.191 Angle : 0.575 9.652 30380 Z= 0.298 Chirality : 0.046 0.356 3307 Planarity : 0.004 0.044 4022 Dihedral : 6.625 83.888 3149 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.08 % Allowed : 14.73 % Favored : 83.19 % 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: -0.21 (0.16), residues: 2743 helix: -0.50 (0.32), residues: 280 sheet: 0.46 (0.16), residues: 1065 loop : -0.47 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1580 HIS 0.003 0.001 HIS A 291 PHE 0.015 0.001 PHE A1242 TYR 0.013 0.001 TYR A2159 ARG 0.009 0.000 ARG A 331 *********************** 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 261 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 211 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 884 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6825 (tp) outliers start: 50 outliers final: 35 residues processed: 247 average time/residue: 1.3243 time to fit residues: 376.3516 Evaluate side-chains 242 residues out of total 2403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 206 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 780 THR 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 2030 ASP Chi-restraints excluded: chain A residue 2106 TYR 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 2332 ASN Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 58 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 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 1054 SER Chi-restraints excluded: chain D residue 1085 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.8481 > 50: distance: 44 - 48: 21.259 distance: 48 - 49: 20.161 distance: 49 - 50: 25.846 distance: 49 - 52: 32.525 distance: 50 - 51: 13.881 distance: 50 - 55: 49.154 distance: 52 - 53: 57.766 distance: 52 - 54: 54.468 distance: 56 - 57: 37.780 distance: 56 - 59: 46.566 distance: 57 - 58: 23.720 distance: 57 - 62: 33.028 distance: 59 - 60: 10.709 distance: 59 - 61: 29.524 distance: 62 - 63: 18.683 distance: 63 - 64: 18.761 distance: 63 - 66: 32.093 distance: 64 - 65: 28.142 distance: 64 - 70: 25.203 distance: 66 - 67: 34.469 distance: 67 - 68: 7.719 distance: 67 - 69: 42.315 distance: 70 - 71: 15.147 distance: 71 - 74: 6.724 distance: 72 - 73: 3.288 distance: 72 - 77: 9.889 distance: 74 - 75: 34.718 distance: 74 - 76: 10.775 distance: 77 - 78: 11.049 distance: 78 - 79: 15.307 distance: 78 - 81: 47.251 distance: 79 - 80: 47.492 distance: 79 - 85: 6.324 distance: 81 - 82: 17.699 distance: 82 - 83: 22.099 distance: 82 - 84: 20.972 distance: 85 - 86: 25.869 distance: 86 - 87: 20.185 distance: 86 - 89: 10.343 distance: 87 - 88: 30.965 distance: 87 - 93: 7.538 distance: 89 - 90: 11.021 distance: 90 - 91: 13.630 distance: 90 - 92: 51.628 distance: 93 - 99: 7.584 distance: 94 - 97: 19.331 distance: 95 - 100: 45.174 distance: 97 - 98: 21.217 distance: 98 - 99: 16.400 distance: 100 - 101: 16.643 distance: 101 - 102: 28.616 distance: 101 - 104: 28.394 distance: 102 - 103: 25.413 distance: 102 - 108: 39.596 distance: 104 - 105: 18.836 distance: 105 - 106: 9.941 distance: 105 - 107: 43.546 distance: 108 - 109: 40.004 distance: 109 - 110: 23.644 distance: 110 - 111: 15.048 distance: 110 - 112: 28.592 distance: 112 - 113: 5.013 distance: 113 - 114: 44.630 distance: 114 - 115: 9.185 distance: 114 - 116: 28.598