Starting phenix.real_space_refine on Sat Apr 13 02:39:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/04_2024/8kd3_37123_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/04_2024/8kd3_37123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/04_2024/8kd3_37123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/04_2024/8kd3_37123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/04_2024/8kd3_37123_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/04_2024/8kd3_37123_updated.pdb" } resolution = 2.9 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= 0.002 sd= 0.011 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 328 5.49 5 S 100 5.16 5 C 16471 2.51 5 N 4897 2.21 5 O 5779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B GLU 816": "OE1" <-> "OE2" Residue "B PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 340": "OE1" <-> "OE2" Residue "O GLU 59": "OE1" <-> "OE2" Residue "O GLU 73": "OE1" <-> "OE2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 56": "OE1" <-> "OE2" Residue "Q GLU 91": "OE1" <-> "OE2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "U GLU 41": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 27576 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3073 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 1 Chain: "B" Number of atoms: 4545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4545 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 12, 'TRANS': 529} Chain breaks: 2 Chain: "D" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1884 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 222} Chain breaks: 2 Chain: "E" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2620 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 18, 'TRANS': 299} Chain breaks: 3 Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1647 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 7, 'TRANS': 192} Chain breaks: 2 Chain: "G" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1043 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain breaks: 2 Chain: "O" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "Q" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "R" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "S" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 848 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "V" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "X" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3384 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "Y" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3340 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.58, per 1000 atoms: 0.49 Number of scatterers: 27576 At special positions: 0 Unit cell: (137.03, 161.17, 188.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 100 16.00 P 328 15.00 O 5779 8.00 N 4897 7.00 C 16471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 303 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS G 263 " - pdb=" SG CYS G 266 " distance=2.03 Simple disulfide: pdb=" SG CYS G 303 " - pdb=" SG CYS G 306 " distance=2.04 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: 12.71 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 188 " 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4866 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 5 sheets defined 49.4% alpha, 2.3% beta 139 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 13.66 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.610A pdb=" N MET A 53 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 54 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 60 removed outlier: 3.517A pdb=" N LYS A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 57 through 60' Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 116 through 136 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 244 through 261 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 288 through 299 removed outlier: 4.011A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 removed outlier: 3.564A pdb=" N ARG A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 366 through 382 removed outlier: 5.070A pdb=" N ASN A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 676 Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 699 through 709 removed outlier: 3.550A pdb=" N PHE B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 724 Processing helix chain 'B' and resid 760 through 763 No H-bonds generated for 'chain 'B' and resid 760 through 763' Processing helix chain 'B' and resid 772 through 777 Processing helix chain 'B' and resid 786 through 790 Processing helix chain 'B' and resid 802 through 840 removed outlier: 3.667A pdb=" N TYR B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 818 " --> pdb=" O ARG B 814 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN B 840 " --> pdb=" O ASN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 862 through 870 Processing helix chain 'B' and resid 873 through 885 removed outlier: 3.963A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 928 removed outlier: 3.996A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 942 removed outlier: 4.035A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.808A pdb=" N ILE B 955 " --> pdb=" O GLU B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 996 Processing helix chain 'B' and resid 1004 through 1021 removed outlier: 3.632A pdb=" N ILE B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1163 Processing helix chain 'B' and resid 1165 through 1173 removed outlier: 3.867A pdb=" N LYS B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1183 Processing helix chain 'B' and resid 1203 through 1216 Processing helix chain 'B' and resid 1222 through 1229 Processing helix chain 'B' and resid 1237 through 1239 No H-bonds generated for 'chain 'B' and resid 1237 through 1239' Processing helix chain 'B' and resid 1242 through 1258 removed outlier: 3.583A pdb=" N THR B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B1258 " --> pdb=" O HIS B1254 " (cutoff:3.500A) Processing helix chain 'B' and resid 1260 through 1272 Processing helix chain 'B' and resid 1283 through 1293 Processing helix chain 'B' and resid 1308 through 1310 No H-bonds generated for 'chain 'B' and resid 1308 through 1310' Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 226 through 240 Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 275 through 292 Processing helix chain 'D' and resid 303 through 315 Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 328 through 343 Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 349 through 369 removed outlier: 3.503A pdb=" N HIS D 369 " --> pdb=" O TRP D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 398 Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 304 through 309 Processing helix chain 'E' and resid 322 through 329 removed outlier: 3.712A pdb=" N ILE E 327 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 344 removed outlier: 4.118A pdb=" N LYS E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 359 Processing helix chain 'E' and resid 383 through 386 No H-bonds generated for 'chain 'E' and resid 383 through 386' Processing helix chain 'E' and resid 403 through 406 Processing helix chain 'E' and resid 431 through 433 No H-bonds generated for 'chain 'E' and resid 431 through 433' Processing helix chain 'E' and resid 544 through 558 Processing helix chain 'F' and resid 99 through 112 Processing helix chain 'F' and resid 230 through 240 removed outlier: 4.074A pdb=" N GLU F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR F 238 " --> pdb=" O ASP F 234 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR F 240 " --> pdb=" O TRP F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 262 removed outlier: 3.847A pdb=" N TYR F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 291 removed outlier: 4.318A pdb=" N TYR F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS F 291 " --> pdb=" O LEU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 312 Processing helix chain 'F' and resid 329 through 342 removed outlier: 4.278A pdb=" N ARG F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) Proline residue: F 339 - end of helix Processing helix chain 'F' and resid 349 through 367 Processing helix chain 'G' and resid 304 through 311 Processing helix chain 'G' and resid 322 through 324 No H-bonds generated for 'chain 'G' and resid 322 through 324' Processing helix chain 'G' and resid 326 through 328 No H-bonds generated for 'chain 'G' and resid 326 through 328' Processing helix chain 'G' and resid 338 through 343 removed outlier: 3.999A pdb=" N ASN G 342 " --> pdb=" O LYS G 338 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 338 through 343' Processing helix chain 'G' and resid 542 through 569 Processing helix chain 'O' and resid 45 through 56 removed outlier: 3.680A pdb=" N LYS O 56 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 77 removed outlier: 3.798A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 113 Processing helix chain 'O' and resid 121 through 131 Processing helix chain 'P' and resid 26 through 28 No H-bonds generated for 'chain 'P' and resid 26 through 28' Processing helix chain 'P' and resid 31 through 40 Processing helix chain 'P' and resid 50 through 75 removed outlier: 3.945A pdb=" N ARG P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 93 removed outlier: 3.977A pdb=" N GLN P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 20 No H-bonds generated for 'chain 'Q' and resid 17 through 20' Processing helix chain 'Q' and resid 27 through 36 Processing helix chain 'Q' and resid 45 through 72 removed outlier: 4.346A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 89 Processing helix chain 'Q' and resid 91 through 96 Processing helix chain 'R' and resid 35 through 45 Processing helix chain 'R' and resid 53 through 80 Processing helix chain 'R' and resid 88 through 98 Processing helix chain 'R' and resid 101 through 118 Processing helix chain 'S' and resid 45 through 55 Processing helix chain 'S' and resid 64 through 78 removed outlier: 3.763A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE S 78 " --> pdb=" O ILE S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 86 through 113 Processing helix chain 'S' and resid 121 through 131 Processing helix chain 'T' and resid 26 through 28 No H-bonds generated for 'chain 'T' and resid 26 through 28' Processing helix chain 'T' and resid 31 through 40 Processing helix chain 'T' and resid 50 through 75 removed outlier: 3.812A pdb=" N ARG T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 91 Processing helix chain 'U' and resid 17 through 20 No H-bonds generated for 'chain 'U' and resid 17 through 20' Processing helix chain 'U' and resid 27 through 35 Processing helix chain 'U' and resid 45 through 72 removed outlier: 4.179A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 89 Processing helix chain 'U' and resid 91 through 96 Processing helix chain 'V' and resid 35 through 45 Processing helix chain 'V' and resid 53 through 80 Processing helix chain 'V' and resid 88 through 98 Processing helix chain 'V' and resid 101 through 118 Processing sheet with id= A, first strand: chain 'A' and resid 62 through 64 removed outlier: 6.528A pdb=" N VAL A 141 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N PHE A 24 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL A 143 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N MET A 305 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ASN A 144 " --> pdb=" O MET A 305 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 307 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL A 267 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 308 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU A 269 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY A 310 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS A 271 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 1136 through 1140 removed outlier: 3.766A pdb=" N ALA B1140 " --> pdb=" O PHE B1301 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B1301 " --> pdb=" O ALA B1140 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 244 through 246 Processing sheet with id= D, first strand: chain 'E' and resid 272 through 274 Processing sheet with id= E, first strand: chain 'E' and resid 437 through 439 845 hydrogen bonds defined for protein. 2454 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 16.35 Time building geometry restraints manager: 13.50 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: 7213 1.34 - 1.46: 7823 1.46 - 1.58: 12964 1.58 - 1.70: 656 1.70 - 1.82: 153 Bond restraints: 28809 Sorted by residual: bond pdb=" CB PRO D 319 " pdb=" CG PRO D 319 " ideal model delta sigma weight residual 1.492 1.677 -0.185 5.00e-02 4.00e+02 1.37e+01 bond pdb=" N ASP E 288 " pdb=" CA ASP E 288 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.24e+01 bond pdb=" N ILE E 395 " pdb=" CA ILE E 395 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.38e+00 bond pdb=" N ILE E 291 " pdb=" CA ILE E 291 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.24e-02 6.50e+03 8.93e+00 bond pdb=" N THR E 396 " pdb=" CA THR E 396 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.99e+00 ... (remaining 28804 not shown) Histogram of bond angle deviations from ideal: 96.73 - 104.27: 1377 104.27 - 111.81: 14056 111.81 - 119.35: 10300 119.35 - 126.89: 13488 126.89 - 134.43: 1064 Bond angle restraints: 40285 Sorted by residual: angle pdb=" CA PRO D 319 " pdb=" N PRO D 319 " pdb=" CD PRO D 319 " ideal model delta sigma weight residual 112.00 97.32 14.68 1.40e+00 5.10e-01 1.10e+02 angle pdb=" CA PRO B 853 " pdb=" N PRO B 853 " pdb=" CD PRO B 853 " ideal model delta sigma weight residual 112.00 102.60 9.40 1.40e+00 5.10e-01 4.51e+01 angle pdb=" CB MET D 107 " pdb=" CG MET D 107 " pdb=" SD MET D 107 " ideal model delta sigma weight residual 112.70 130.10 -17.40 3.00e+00 1.11e-01 3.36e+01 angle pdb=" CA MET D 107 " pdb=" CB MET D 107 " pdb=" CG MET D 107 " ideal model delta sigma weight residual 114.10 125.29 -11.19 2.00e+00 2.50e-01 3.13e+01 angle pdb=" CB MET O 90 " pdb=" CG MET O 90 " pdb=" SD MET O 90 " ideal model delta sigma weight residual 112.70 128.61 -15.91 3.00e+00 1.11e-01 2.81e+01 ... (remaining 40280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 14402 35.15 - 70.29: 2026 70.29 - 105.44: 60 105.44 - 140.59: 2 140.59 - 175.74: 1 Dihedral angle restraints: 16491 sinusoidal: 8965 harmonic: 7526 Sorted by residual: dihedral pdb=" CB CYS G 263 " pdb=" SG CYS G 263 " pdb=" SG CYS G 266 " pdb=" CB CYS G 266 " ideal model delta sinusoidal sigma weight residual 93.00 46.45 46.55 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA GLU B1220 " pdb=" C GLU B1220 " pdb=" N HIS B1221 " pdb=" CA HIS B1221 " ideal model delta harmonic sigma weight residual -180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" C MET D 107 " pdb=" N MET D 107 " pdb=" CA MET D 107 " pdb=" CB MET D 107 " ideal model delta harmonic sigma weight residual -122.60 -132.87 10.27 0 2.50e+00 1.60e-01 1.69e+01 ... (remaining 16488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4154 0.081 - 0.161: 267 0.161 - 0.242: 17 0.242 - 0.323: 3 0.323 - 0.403: 1 Chirality restraints: 4442 Sorted by residual: chirality pdb=" CA ILE E 395 " pdb=" N ILE E 395 " pdb=" C ILE E 395 " pdb=" CB ILE E 395 " both_signs ideal model delta sigma weight residual False 2.43 2.84 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CB ILE F 105 " pdb=" CA ILE F 105 " pdb=" CG1 ILE F 105 " pdb=" CG2 ILE F 105 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA MET D 107 " pdb=" N MET D 107 " pdb=" C MET D 107 " pdb=" CB MET D 107 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 4439 not shown) Planarity restraints: 3978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 852 " -0.095 5.00e-02 4.00e+02 1.37e-01 3.02e+01 pdb=" N PRO B 853 " 0.237 5.00e-02 4.00e+02 pdb=" CA PRO B 853 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 853 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 318 " 0.073 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO D 319 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 88 " -0.023 2.00e-02 2.50e+03 2.70e-02 1.45e+01 pdb=" CG TYR P 88 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR P 88 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR P 88 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR P 88 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR P 88 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR P 88 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR P 88 " 0.000 2.00e-02 2.50e+03 ... (remaining 3975 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 5 2.01 - 2.73: 1580 2.73 - 3.45: 38416 3.45 - 4.18: 73271 4.18 - 4.90: 117444 Nonbonded interactions: 230716 Sorted by model distance: nonbonded pdb=" OE2 GLU B 885 " pdb=" CD2 HIS B 886 " model vdw 1.281 3.260 nonbonded pdb=" NE2 HIS O 113 " pdb=" OD1 ASP S 123 " model vdw 1.391 2.520 nonbonded pdb=" OD1 ASP B 872 " pdb=" O ILE E 54 " model vdw 1.709 3.040 nonbonded pdb=" CB ALA A 36 " pdb=" CD2 LEU E 48 " model vdw 1.813 3.880 nonbonded pdb=" OE2 GLU B 816 " pdb=" OD1 ASP E 47 " model vdw 1.850 3.040 ... (remaining 230711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 11 through 24 or resid 80 through 113 or resid 222 through \ 373)) selection = chain 'F' } ncs_group { reference = (chain 'O' and resid 36 through 133) selection = (chain 'S' and resid 36 through 133) } ncs_group { reference = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = (chain 'R' and resid 29 through 119) selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 10.310 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: 33.950 Check model and map are aligned: 0.470 Set scattering table: 0.250 Process input model: 92.260 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.160 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:15.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 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 0.185 28809 Z= 0.236 Angle : 0.772 17.397 40285 Z= 0.425 Chirality : 0.043 0.403 4442 Planarity : 0.006 0.137 3978 Dihedral : 24.414 175.735 11616 Min Nonbonded Distance : 1.281 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.13 % Allowed : 30.60 % Favored : 69.27 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.16), residues: 2507 helix: -0.20 (0.13), residues: 1350 sheet: 0.83 (0.61), residues: 93 loop : -1.83 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP F 365 HIS 0.005 0.001 HIS R 46 PHE 0.023 0.001 PHE B 985 TYR 0.066 0.001 TYR P 88 ARG 0.024 0.001 ARG U 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 324 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 THR cc_start: 0.8387 (t) cc_final: 0.8034 (m) REVERT: D 107 MET cc_start: 0.7324 (ttt) cc_final: 0.7025 (mmp) REVERT: D 223 GLN cc_start: 0.6619 (pp30) cc_final: 0.6350 (pp30) REVERT: F 307 ASP cc_start: 0.4858 (t70) cc_final: 0.4589 (t70) REVERT: F 340 GLU cc_start: 0.4745 (pm20) cc_final: 0.4526 (tm-30) outliers start: 3 outliers final: 0 residues processed: 326 average time/residue: 1.2741 time to fit residues: 491.9822 Evaluate side-chains 280 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 237 optimal weight: 0.7980 chunk 212 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 220 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 690 ASN B 886 HIS ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 402 ASN E 517 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 GLN O 39 HIS S 85 GLN S 93 GLN T 25 ASN V 60 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 28809 Z= 0.248 Angle : 0.591 10.914 40285 Z= 0.321 Chirality : 0.038 0.214 4442 Planarity : 0.004 0.067 3978 Dihedral : 26.323 175.065 6379 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.27 % Allowed : 25.59 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.16), residues: 2507 helix: 0.50 (0.14), residues: 1375 sheet: 0.56 (0.60), residues: 98 loop : -1.58 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 365 HIS 0.009 0.001 HIS B 886 PHE 0.015 0.002 PHE A 215 TYR 0.021 0.002 TYR F 299 ARG 0.010 0.001 ARG U 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 334 time to evaluate : 3.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8511 (t0) cc_final: 0.7955 (t0) REVERT: A 128 MET cc_start: 0.8903 (mtm) cc_final: 0.8612 (mtm) REVERT: A 326 THR cc_start: 0.8807 (m) cc_final: 0.8573 (m) REVERT: A 373 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7098 (mpp) REVERT: B 1299 ASN cc_start: 0.6536 (OUTLIER) cc_final: 0.6219 (m-40) REVERT: D 309 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7319 (mt) REVERT: D 357 LYS cc_start: 0.8280 (tptt) cc_final: 0.7895 (ttmt) REVERT: D 368 MET cc_start: 0.7007 (mmm) cc_final: 0.6652 (mmp) REVERT: E 371 GLN cc_start: 0.8708 (pm20) cc_final: 0.8430 (pm20) REVERT: E 387 PHE cc_start: 0.7088 (OUTLIER) cc_final: 0.6556 (m-80) REVERT: E 548 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8124 (ptpp) REVERT: F 237 GLU cc_start: 0.4353 (tp30) cc_final: 0.2334 (mt-10) REVERT: F 307 ASP cc_start: 0.4880 (t70) cc_final: 0.4626 (t70) REVERT: F 368 MET cc_start: 0.3870 (OUTLIER) cc_final: 0.2325 (ppp) REVERT: P 40 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.7999 (ttp-170) REVERT: P 44 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8292 (tmtt) REVERT: Q 90 ASP cc_start: 0.8289 (t0) cc_final: 0.8053 (t70) REVERT: R 45 VAL cc_start: 0.8311 (p) cc_final: 0.8067 (m) REVERT: R 53 SER cc_start: 0.9239 (p) cc_final: 0.8865 (m) outliers start: 120 outliers final: 37 residues processed: 410 average time/residue: 1.3887 time to fit residues: 666.4293 Evaluate side-chains 347 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 302 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1266 MET Chi-restraints excluded: chain B residue 1299 ASN Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 548 LYS Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 44 LYS Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 141 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 255 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 227 optimal weight: 0.5980 chunk 253 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 GLN G 302 HIS O 39 HIS P 25 ASN T 25 ASN U 73 ASN U 104 GLN ** V 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 28809 Z= 0.347 Angle : 0.647 11.398 40285 Z= 0.351 Chirality : 0.042 0.308 4442 Planarity : 0.005 0.147 3978 Dihedral : 26.782 175.201 6379 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.19 % Favored : 95.77 % Rotamer: Outliers : 5.44 % Allowed : 25.20 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2507 helix: 0.34 (0.14), residues: 1378 sheet: 0.07 (0.57), residues: 93 loop : -1.48 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 775 HIS 0.007 0.001 HIS B 815 PHE 0.026 0.002 PHE A 85 TYR 0.036 0.002 TYR P 88 ARG 0.017 0.001 ARG V 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 346 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8994 (mtm) cc_final: 0.8772 (mtp) REVERT: A 189 HIS cc_start: 0.7534 (OUTLIER) cc_final: 0.6837 (p90) REVERT: A 248 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7752 (mmm-85) REVERT: A 261 TRP cc_start: 0.7720 (m-10) cc_final: 0.7398 (m-90) REVERT: A 298 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8468 (t) REVERT: A 326 THR cc_start: 0.9015 (m) cc_final: 0.8803 (m) REVERT: A 367 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: B 674 ARG cc_start: 0.8067 (mtp180) cc_final: 0.7833 (mtp-110) REVERT: B 821 ILE cc_start: 0.8659 (mt) cc_final: 0.8457 (mp) REVERT: B 1182 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.6979 (mmtm) REVERT: D 109 LYS cc_start: 0.3626 (OUTLIER) cc_final: 0.2777 (ptmt) REVERT: D 357 LYS cc_start: 0.8394 (tptt) cc_final: 0.8149 (ttmt) REVERT: D 368 MET cc_start: 0.7459 (mmm) cc_final: 0.7170 (mmp) REVERT: D 395 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7831 (tm-30) REVERT: E 371 GLN cc_start: 0.8852 (pm20) cc_final: 0.8389 (pm20) REVERT: E 387 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6558 (m-80) REVERT: E 407 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8348 (mm) REVERT: E 557 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7614 (pptt) REVERT: F 307 ASP cc_start: 0.4917 (t70) cc_final: 0.4616 (t70) REVERT: F 368 MET cc_start: 0.2811 (OUTLIER) cc_final: 0.1878 (tpt) REVERT: O 120 MET cc_start: 0.8696 (mmm) cc_final: 0.7986 (mtm) REVERT: P 84 MET cc_start: 0.8989 (tpp) cc_final: 0.8745 (mmt) REVERT: Q 90 ASP cc_start: 0.8371 (t0) cc_final: 0.8120 (t70) REVERT: R 53 SER cc_start: 0.9217 (p) cc_final: 0.8944 (m) REVERT: R 68 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7815 (mt-10) REVERT: U 29 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.7346 (ttp80) REVERT: U 73 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8395 (m110) REVERT: U 79 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8664 (pt) REVERT: U 90 ASP cc_start: 0.8276 (t70) cc_final: 0.7978 (t0) REVERT: V 46 HIS cc_start: 0.8475 (OUTLIER) cc_final: 0.8220 (m170) outliers start: 124 outliers final: 39 residues processed: 424 average time/residue: 1.5668 time to fit residues: 765.8604 Evaluate side-chains 356 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 304 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1182 LYS Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 371 ASP Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 252 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 122 optimal weight: 0.0980 chunk 171 optimal weight: 20.0000 chunk 256 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 243 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 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 76 GLN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN D 295 ASN D 393 GLN E 352 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN V 60 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28809 Z= 0.264 Angle : 0.567 10.993 40285 Z= 0.311 Chirality : 0.037 0.170 4442 Planarity : 0.004 0.054 3978 Dihedral : 26.651 174.844 6379 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.70 % Allowed : 26.51 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 2507 helix: 0.55 (0.14), residues: 1386 sheet: -0.27 (0.55), residues: 93 loop : -1.43 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 775 HIS 0.007 0.001 HIS A 188 PHE 0.017 0.001 PHE B 708 TYR 0.035 0.002 TYR P 88 ARG 0.009 0.000 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 308 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8999 (mtm) cc_final: 0.8795 (mtp) REVERT: A 189 HIS cc_start: 0.7427 (OUTLIER) cc_final: 0.6589 (p90) REVERT: A 211 TYR cc_start: 0.7671 (t80) cc_final: 0.7455 (t80) REVERT: A 248 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8080 (mmm-85) REVERT: A 261 TRP cc_start: 0.7760 (m-10) cc_final: 0.7397 (m-90) REVERT: A 306 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8494 (ttm) REVERT: B 805 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7787 (mp0) REVERT: D 107 MET cc_start: 0.5358 (tpt) cc_final: 0.5094 (pp-130) REVERT: D 357 LYS cc_start: 0.8430 (tptt) cc_final: 0.8174 (ttmt) REVERT: D 368 MET cc_start: 0.7500 (mmm) cc_final: 0.7298 (mmp) REVERT: D 395 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7868 (tm-30) REVERT: E 371 GLN cc_start: 0.8820 (pm20) cc_final: 0.8304 (pm20) REVERT: E 387 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: E 557 LYS cc_start: 0.7555 (mmtt) cc_final: 0.7325 (pptt) REVERT: F 96 ARG cc_start: 0.1442 (OUTLIER) cc_final: -0.1508 (mmt180) REVERT: F 107 MET cc_start: 0.0268 (OUTLIER) cc_final: -0.0266 (ptt) REVERT: F 288 TYR cc_start: 0.5116 (OUTLIER) cc_final: 0.4216 (t80) REVERT: F 307 ASP cc_start: 0.4933 (t70) cc_final: 0.4637 (t70) REVERT: F 368 MET cc_start: 0.3511 (OUTLIER) cc_final: 0.2018 (tpt) REVERT: G 316 MET cc_start: 0.3431 (mtt) cc_final: 0.3185 (mtm) REVERT: O 120 MET cc_start: 0.8674 (mmm) cc_final: 0.8065 (mtm) REVERT: P 50 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8369 (tt) REVERT: P 84 MET cc_start: 0.8876 (tpp) cc_final: 0.8589 (mmt) REVERT: Q 24 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8863 (mm-40) REVERT: Q 51 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9073 (tp) REVERT: Q 73 ASN cc_start: 0.8707 (t0) cc_final: 0.8438 (t0) REVERT: Q 90 ASP cc_start: 0.8381 (t0) cc_final: 0.8112 (t70) REVERT: R 83 ARG cc_start: 0.8145 (mtt90) cc_final: 0.7893 (mmt90) REVERT: U 23 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8497 (mp) REVERT: U 29 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.7423 (ttp80) REVERT: U 79 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8529 (pt) REVERT: U 90 ASP cc_start: 0.8204 (t70) cc_final: 0.7923 (t0) REVERT: V 46 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.8266 (m170) REVERT: V 58 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8988 (mp) outliers start: 107 outliers final: 39 residues processed: 382 average time/residue: 1.4681 time to fit residues: 651.8422 Evaluate side-chains 346 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 292 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1230 GLN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 288 TYR Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 226 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 202 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 243 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN ** S 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN V 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28809 Z= 0.225 Angle : 0.554 12.779 40285 Z= 0.303 Chirality : 0.036 0.181 4442 Planarity : 0.004 0.053 3978 Dihedral : 26.605 174.798 6379 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.39 % Allowed : 26.78 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2507 helix: 0.69 (0.14), residues: 1385 sheet: -0.71 (0.52), residues: 101 loop : -1.39 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 719 HIS 0.006 0.001 HIS B 815 PHE 0.014 0.001 PHE A 160 TYR 0.036 0.001 TYR P 88 ARG 0.008 0.000 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 297 time to evaluate : 3.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: A 189 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.6567 (p90) REVERT: A 211 TYR cc_start: 0.7653 (t80) cc_final: 0.7414 (t80) REVERT: A 248 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8074 (mmm-85) REVERT: A 261 TRP cc_start: 0.7788 (m-10) cc_final: 0.7419 (m-90) REVERT: A 367 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: B 697 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8776 (mp) REVERT: B 805 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7761 (mp0) REVERT: B 821 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8370 (mm) REVERT: B 982 LYS cc_start: 0.7207 (mtmt) cc_final: 0.6981 (tttt) REVERT: D 107 MET cc_start: 0.5606 (tpt) cc_final: 0.5237 (pp-130) REVERT: D 357 LYS cc_start: 0.8420 (tptt) cc_final: 0.8158 (ttmt) REVERT: D 395 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7846 (tm-30) REVERT: E 371 GLN cc_start: 0.8827 (pm20) cc_final: 0.8299 (pm20) REVERT: F 96 ARG cc_start: 0.1471 (OUTLIER) cc_final: -0.1477 (mmt180) REVERT: F 107 MET cc_start: 0.0281 (OUTLIER) cc_final: -0.0239 (ptt) REVERT: F 288 TYR cc_start: 0.5101 (OUTLIER) cc_final: 0.4171 (t80) REVERT: F 307 ASP cc_start: 0.5012 (t70) cc_final: 0.4732 (t70) REVERT: F 368 MET cc_start: 0.3746 (OUTLIER) cc_final: 0.2093 (tpt) REVERT: G 316 MET cc_start: 0.3372 (mtt) cc_final: 0.3136 (mtm) REVERT: O 120 MET cc_start: 0.8727 (mmm) cc_final: 0.8039 (mtm) REVERT: P 50 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8343 (tt) REVERT: Q 73 ASN cc_start: 0.8709 (t0) cc_final: 0.8393 (t0) REVERT: Q 90 ASP cc_start: 0.8374 (t0) cc_final: 0.8110 (t70) REVERT: R 68 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8058 (mm-30) REVERT: R 83 ARG cc_start: 0.8127 (mtt90) cc_final: 0.7890 (mmt90) REVERT: U 23 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8468 (mp) REVERT: U 29 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.7449 (ttp80) REVERT: U 73 ASN cc_start: 0.8476 (t0) cc_final: 0.8220 (m110) REVERT: U 75 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8756 (mttm) REVERT: U 90 ASP cc_start: 0.8174 (t70) cc_final: 0.7891 (t0) REVERT: V 58 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8985 (mp) outliers start: 100 outliers final: 43 residues processed: 370 average time/residue: 1.5129 time to fit residues: 650.0293 Evaluate side-chains 346 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 288 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1230 GLN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 288 TYR Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 91 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 67 optimal weight: 0.0030 chunk 271 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN B1230 GLN E 350 GLN E 519 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 108 ASN T 25 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 28809 Z= 0.438 Angle : 0.676 11.967 40285 Z= 0.367 Chirality : 0.043 0.306 4442 Planarity : 0.005 0.070 3978 Dihedral : 27.004 175.799 6379 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.18 % Allowed : 26.08 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.16), residues: 2507 helix: 0.34 (0.14), residues: 1392 sheet: -1.13 (0.52), residues: 91 loop : -1.44 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 719 HIS 0.009 0.002 HIS V 46 PHE 0.026 0.002 PHE A 160 TYR 0.035 0.002 TYR A 347 ARG 0.011 0.001 ARG V 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 325 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.6997 (mttm) cc_final: 0.6626 (mtpp) REVERT: A 97 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6534 (t80) REVERT: A 189 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.7464 (p90) REVERT: A 248 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7997 (mmm-85) REVERT: A 261 TRP cc_start: 0.7934 (m-10) cc_final: 0.7505 (m-90) REVERT: A 367 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: B 697 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8723 (mp) REVERT: B 765 MET cc_start: 0.3575 (OUTLIER) cc_final: 0.2740 (tpp) REVERT: B 821 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8464 (mp) REVERT: B 982 LYS cc_start: 0.7444 (mtmt) cc_final: 0.7225 (tttt) REVERT: B 1182 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7429 (mmmm) REVERT: B 1288 LEU cc_start: 0.8175 (mp) cc_final: 0.7949 (mp) REVERT: D 107 MET cc_start: 0.5613 (tpt) cc_final: 0.5279 (pp-130) REVERT: D 357 LYS cc_start: 0.8488 (tptt) cc_final: 0.8252 (ttmt) REVERT: D 371 ASP cc_start: 0.7335 (t0) cc_final: 0.7077 (OUTLIER) REVERT: D 395 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7920 (tm-30) REVERT: E 371 GLN cc_start: 0.8900 (pm20) cc_final: 0.8310 (pm20) REVERT: E 387 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.5947 (t80) REVERT: F 96 ARG cc_start: 0.1570 (OUTLIER) cc_final: -0.1363 (mmt180) REVERT: F 107 MET cc_start: 0.0381 (OUTLIER) cc_final: -0.0164 (ptt) REVERT: F 307 ASP cc_start: 0.5165 (t70) cc_final: 0.4871 (t70) REVERT: F 368 MET cc_start: 0.3915 (OUTLIER) cc_final: 0.2245 (tpt) REVERT: G 316 MET cc_start: 0.3424 (mtt) cc_final: 0.3147 (mtm) REVERT: O 120 MET cc_start: 0.8814 (mmm) cc_final: 0.8034 (mtm) REVERT: Q 56 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8729 (tt0) REVERT: Q 73 ASN cc_start: 0.8727 (t0) cc_final: 0.8357 (t0) REVERT: Q 90 ASP cc_start: 0.8435 (t0) cc_final: 0.8168 (t70) REVERT: R 68 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8076 (mm-30) REVERT: S 87 SER cc_start: 0.9279 (t) cc_final: 0.9060 (p) REVERT: U 23 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8648 (mp) REVERT: U 29 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.7563 (ttp80) REVERT: U 64 GLU cc_start: 0.8251 (tt0) cc_final: 0.7912 (tp30) REVERT: U 73 ASN cc_start: 0.8566 (t0) cc_final: 0.8312 (m110) REVERT: U 90 ASP cc_start: 0.8273 (t70) cc_final: 0.7974 (t0) REVERT: V 83 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7593 (mpt-90) outliers start: 118 outliers final: 48 residues processed: 400 average time/residue: 1.5511 time to fit residues: 715.0781 Evaluate side-chains 357 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 294 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1182 LYS Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 83 ARG Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 262 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 154 optimal weight: 20.0000 chunk 198 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 228 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 270 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 125 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS D 295 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN O 68 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN T 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28809 Z= 0.205 Angle : 0.567 11.004 40285 Z= 0.311 Chirality : 0.037 0.186 4442 Planarity : 0.004 0.053 3978 Dihedral : 26.804 174.033 6379 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.51 % Allowed : 27.70 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 2507 helix: 0.58 (0.14), residues: 1400 sheet: -0.71 (0.56), residues: 83 loop : -1.38 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 719 HIS 0.013 0.001 HIS B1254 PHE 0.018 0.001 PHE A 160 TYR 0.033 0.001 TYR P 88 ARG 0.010 0.000 ARG V 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 310 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7049 (mttm) cc_final: 0.6645 (mtpp) REVERT: A 97 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6283 (t80) REVERT: A 165 ASP cc_start: 0.8012 (p0) cc_final: 0.7555 (p0) REVERT: A 189 HIS cc_start: 0.7542 (OUTLIER) cc_final: 0.6666 (p90) REVERT: A 248 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7999 (mmm-85) REVERT: A 261 TRP cc_start: 0.7898 (m-10) cc_final: 0.7400 (m-90) REVERT: A 367 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: B 765 MET cc_start: 0.3956 (tmm) cc_final: 0.3333 (tpp) REVERT: B 821 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8396 (mp) REVERT: B 982 LYS cc_start: 0.7380 (mtmt) cc_final: 0.7133 (tttt) REVERT: B 1288 LEU cc_start: 0.8180 (mp) cc_final: 0.7951 (mp) REVERT: D 107 MET cc_start: 0.5777 (tpt) cc_final: 0.5401 (pp-130) REVERT: D 357 LYS cc_start: 0.8476 (tptt) cc_final: 0.8226 (ttmt) REVERT: D 371 ASP cc_start: 0.7240 (t0) cc_final: 0.6975 (OUTLIER) REVERT: D 395 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7871 (tm-30) REVERT: E 371 GLN cc_start: 0.8851 (pm20) cc_final: 0.8284 (pm20) REVERT: E 387 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.5906 (t80) REVERT: F 96 ARG cc_start: 0.1562 (OUTLIER) cc_final: -0.1366 (mmt180) REVERT: F 107 MET cc_start: 0.0384 (OUTLIER) cc_final: -0.0099 (ptt) REVERT: F 235 ASP cc_start: 0.5017 (OUTLIER) cc_final: 0.4736 (t0) REVERT: F 307 ASP cc_start: 0.5106 (t70) cc_final: 0.4806 (t70) REVERT: F 368 MET cc_start: 0.3091 (ppp) cc_final: 0.1957 (tpt) REVERT: G 316 MET cc_start: 0.3321 (mtt) cc_final: 0.3036 (mtm) REVERT: O 120 MET cc_start: 0.8674 (mmm) cc_final: 0.7997 (mtm) REVERT: P 50 ILE cc_start: 0.8464 (tt) cc_final: 0.8232 (tt) REVERT: Q 73 ASN cc_start: 0.8672 (t0) cc_final: 0.8258 (t0) REVERT: Q 90 ASP cc_start: 0.8398 (t0) cc_final: 0.8131 (t70) REVERT: R 68 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8012 (mm-30) REVERT: U 23 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8450 (mp) REVERT: U 29 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.7557 (ttp80) REVERT: U 79 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8520 (pt) REVERT: U 90 ASP cc_start: 0.8138 (t70) cc_final: 0.7863 (t0) REVERT: V 68 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: V 90 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8277 (mp0) outliers start: 80 outliers final: 34 residues processed: 367 average time/residue: 1.5576 time to fit residues: 660.9826 Evaluate side-chains 344 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 297 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 90 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 167 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1222 GLN D 295 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN T 25 ASN V 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.6301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 28809 Z= 0.421 Angle : 0.661 12.010 40285 Z= 0.359 Chirality : 0.042 0.255 4442 Planarity : 0.005 0.066 3978 Dihedral : 27.112 176.064 6379 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.95 % Favored : 95.01 % Rotamer: Outliers : 4.04 % Allowed : 26.95 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2507 helix: 0.36 (0.14), residues: 1401 sheet: -1.37 (0.54), residues: 81 loop : -1.41 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 719 HIS 0.009 0.001 HIS B 815 PHE 0.031 0.002 PHE A 160 TYR 0.033 0.002 TYR P 88 ARG 0.015 0.001 ARG U 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 301 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.6619 (t80) REVERT: A 165 ASP cc_start: 0.8081 (p0) cc_final: 0.7650 (p0) REVERT: A 189 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7448 (p90) REVERT: A 248 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7997 (mmm-85) REVERT: A 261 TRP cc_start: 0.7970 (m-10) cc_final: 0.7467 (m-90) REVERT: A 367 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: B 700 ASP cc_start: 0.8563 (m-30) cc_final: 0.8305 (m-30) REVERT: B 821 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8461 (mp) REVERT: B 982 LYS cc_start: 0.7451 (mtmt) cc_final: 0.7235 (tttt) REVERT: B 1182 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7433 (mmmm) REVERT: B 1222 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7546 (pt0) REVERT: B 1288 LEU cc_start: 0.8292 (mp) cc_final: 0.8080 (mp) REVERT: D 22 MET cc_start: 0.6612 (mtt) cc_final: 0.6130 (mpt) REVERT: D 107 MET cc_start: 0.5776 (tpt) cc_final: 0.5408 (pp-130) REVERT: D 357 LYS cc_start: 0.8491 (tptt) cc_final: 0.8270 (ttmt) REVERT: D 395 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7920 (tm-30) REVERT: E 387 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.5940 (t80) REVERT: E 407 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8532 (mm) REVERT: F 96 ARG cc_start: 0.1551 (OUTLIER) cc_final: -0.1300 (mmt180) REVERT: F 107 MET cc_start: 0.0374 (OUTLIER) cc_final: -0.0218 (ptt) REVERT: F 235 ASP cc_start: 0.5076 (OUTLIER) cc_final: 0.4790 (t0) REVERT: F 307 ASP cc_start: 0.5202 (t70) cc_final: 0.4918 (t70) REVERT: F 368 MET cc_start: 0.3434 (ppp) cc_final: 0.2138 (tpt) REVERT: G 316 MET cc_start: 0.3511 (mtt) cc_final: 0.3208 (mtm) REVERT: O 68 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: O 120 MET cc_start: 0.8870 (mmm) cc_final: 0.7989 (mtm) REVERT: Q 56 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8713 (tt0) REVERT: Q 73 ASN cc_start: 0.8695 (t0) cc_final: 0.8349 (t0) REVERT: Q 90 ASP cc_start: 0.8409 (t0) cc_final: 0.8147 (t70) REVERT: R 68 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8080 (mm-30) REVERT: T 77 LYS cc_start: 0.8702 (mmtm) cc_final: 0.8361 (mmpt) REVERT: U 29 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.7578 (ttp80) REVERT: U 64 GLU cc_start: 0.8232 (tt0) cc_final: 0.7906 (tp30) REVERT: U 79 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8573 (pt) REVERT: U 90 ASP cc_start: 0.8270 (t70) cc_final: 0.7966 (t0) REVERT: V 81 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8289 (m110) outliers start: 92 outliers final: 42 residues processed: 363 average time/residue: 1.5387 time to fit residues: 644.5101 Evaluate side-chains 347 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 288 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 881 ASP Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1182 LYS Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1222 GLN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 81 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 246 optimal weight: 0.5980 chunk 259 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 198 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 228 optimal weight: 0.5980 chunk 238 optimal weight: 0.9990 chunk 251 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28809 Z= 0.233 Angle : 0.597 15.299 40285 Z= 0.324 Chirality : 0.038 0.183 4442 Planarity : 0.004 0.057 3978 Dihedral : 26.958 173.934 6379 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.65 % Rotamer: Outliers : 2.99 % Allowed : 28.58 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2507 helix: 0.51 (0.14), residues: 1401 sheet: -0.87 (0.59), residues: 73 loop : -1.39 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 719 HIS 0.010 0.001 HIS B1221 PHE 0.026 0.001 PHE A 160 TYR 0.038 0.002 TYR P 88 ARG 0.014 0.000 ARG U 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 303 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.6873 (t80) REVERT: A 165 ASP cc_start: 0.8021 (p0) cc_final: 0.7596 (p0) REVERT: A 189 HIS cc_start: 0.7663 (OUTLIER) cc_final: 0.6795 (p90) REVERT: A 211 TYR cc_start: 0.7807 (t80) cc_final: 0.7531 (t80) REVERT: A 248 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7994 (mmm-85) REVERT: A 261 TRP cc_start: 0.7925 (m-10) cc_final: 0.7395 (m-90) REVERT: A 367 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: B 700 ASP cc_start: 0.8550 (m-30) cc_final: 0.8294 (m-30) REVERT: B 975 LEU cc_start: 0.8481 (tt) cc_final: 0.8246 (tp) REVERT: B 982 LYS cc_start: 0.7427 (mtmt) cc_final: 0.7209 (tttt) REVERT: B 1182 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7440 (mmmm) REVERT: B 1288 LEU cc_start: 0.8170 (mp) cc_final: 0.7968 (mp) REVERT: D 22 MET cc_start: 0.6617 (mtt) cc_final: 0.6154 (mpt) REVERT: D 107 MET cc_start: 0.5795 (tpt) cc_final: 0.5405 (pp-130) REVERT: D 357 LYS cc_start: 0.8471 (tptt) cc_final: 0.8219 (ttmt) REVERT: D 395 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7855 (tm-30) REVERT: E 371 GLN cc_start: 0.8871 (pm20) cc_final: 0.8344 (pm20) REVERT: E 387 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.5821 (t80) REVERT: F 96 ARG cc_start: 0.1651 (OUTLIER) cc_final: -0.1280 (mmt180) REVERT: F 107 MET cc_start: 0.0395 (OUTLIER) cc_final: -0.0191 (ptt) REVERT: F 235 ASP cc_start: 0.5056 (OUTLIER) cc_final: 0.4778 (t0) REVERT: F 307 ASP cc_start: 0.5166 (t70) cc_final: 0.4883 (t70) REVERT: F 368 MET cc_start: 0.3387 (ppp) cc_final: 0.2218 (tpt) REVERT: G 316 MET cc_start: 0.3508 (mtt) cc_final: 0.3226 (mtm) REVERT: O 68 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: O 120 MET cc_start: 0.8745 (mmm) cc_final: 0.7872 (mtm) REVERT: Q 56 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8660 (tt0) REVERT: Q 73 ASN cc_start: 0.8667 (t0) cc_final: 0.8306 (t0) REVERT: Q 90 ASP cc_start: 0.8367 (t0) cc_final: 0.8113 (t70) REVERT: R 44 GLN cc_start: 0.8702 (tt0) cc_final: 0.8479 (tt0) REVERT: R 68 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8056 (mm-30) REVERT: T 77 LYS cc_start: 0.8485 (mmtm) cc_final: 0.8222 (mmpt) REVERT: U 29 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.7611 (ttp80) REVERT: U 79 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8505 (pt) REVERT: U 90 ASP cc_start: 0.8180 (t70) cc_final: 0.7900 (t0) outliers start: 68 outliers final: 43 residues processed: 354 average time/residue: 1.5354 time to fit residues: 629.8648 Evaluate side-chains 343 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 287 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 881 ASP Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1011 LYS Chi-restraints excluded: chain B residue 1182 LYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 478 ILE Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 81 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 165 optimal weight: 50.0000 chunk 266 optimal weight: 5.9990 chunk 162 optimal weight: 0.0020 chunk 126 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 222 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 172 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN V 60 ASN V 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.6209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 28809 Z= 0.265 Angle : 0.604 14.303 40285 Z= 0.327 Chirality : 0.038 0.235 4442 Planarity : 0.004 0.061 3978 Dihedral : 26.890 175.281 6379 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 2.90 % Allowed : 28.49 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2507 helix: 0.58 (0.14), residues: 1401 sheet: -0.79 (0.59), residues: 73 loop : -1.38 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 719 HIS 0.007 0.001 HIS A 188 PHE 0.031 0.001 PHE A 160 TYR 0.042 0.002 TYR P 88 ARG 0.014 0.000 ARG U 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 290 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.6831 (t80) REVERT: A 165 ASP cc_start: 0.8076 (p0) cc_final: 0.7628 (p0) REVERT: A 189 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.6883 (p90) REVERT: A 248 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7970 (mmm-85) REVERT: A 261 TRP cc_start: 0.7906 (m-10) cc_final: 0.7363 (m-90) REVERT: A 367 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: B 700 ASP cc_start: 0.8555 (m-30) cc_final: 0.8310 (m-30) REVERT: B 1182 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7481 (mmmm) REVERT: D 22 MET cc_start: 0.6594 (mtt) cc_final: 0.6142 (mpt) REVERT: D 107 MET cc_start: 0.5803 (tpt) cc_final: 0.5467 (pp-130) REVERT: D 357 LYS cc_start: 0.8456 (tptt) cc_final: 0.8202 (ttmt) REVERT: D 395 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7873 (tm-30) REVERT: E 371 GLN cc_start: 0.8880 (pm20) cc_final: 0.8351 (pm20) REVERT: E 387 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.5799 (t80) REVERT: F 96 ARG cc_start: 0.1567 (OUTLIER) cc_final: -0.1253 (mmt180) REVERT: F 107 MET cc_start: 0.0307 (OUTLIER) cc_final: -0.0250 (ptt) REVERT: F 235 ASP cc_start: 0.5054 (OUTLIER) cc_final: 0.4769 (t0) REVERT: F 307 ASP cc_start: 0.5174 (t70) cc_final: 0.4888 (t70) REVERT: F 368 MET cc_start: 0.3464 (ppp) cc_final: 0.2339 (tpt) REVERT: G 316 MET cc_start: 0.3452 (mtt) cc_final: 0.3154 (mtm) REVERT: O 120 MET cc_start: 0.8828 (mmm) cc_final: 0.7901 (mtm) REVERT: Q 56 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8686 (tt0) REVERT: Q 73 ASN cc_start: 0.8665 (t0) cc_final: 0.8311 (t0) REVERT: Q 90 ASP cc_start: 0.8344 (t0) cc_final: 0.8090 (t70) REVERT: R 44 GLN cc_start: 0.8693 (tt0) cc_final: 0.8443 (tt0) REVERT: R 68 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8041 (mm-30) REVERT: T 77 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8235 (mmpt) REVERT: U 23 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8490 (mp) REVERT: U 29 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.7616 (ttp80) REVERT: U 79 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8511 (pt) REVERT: U 90 ASP cc_start: 0.8158 (t70) cc_final: 0.7874 (t0) outliers start: 66 outliers final: 46 residues processed: 336 average time/residue: 1.5581 time to fit residues: 603.6066 Evaluate side-chains 343 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 284 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 881 ASP Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1011 LYS Chi-restraints excluded: chain B residue 1182 LYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 368 MET Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 81 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 177 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 229 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 ASN V 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.125806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.092511 restraints weight = 54935.495| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.93 r_work: 0.3156 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28809 Z= 0.235 Angle : 0.601 14.464 40285 Z= 0.323 Chirality : 0.037 0.196 4442 Planarity : 0.004 0.058 3978 Dihedral : 26.830 174.666 6379 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.63 % Favored : 95.33 % Rotamer: Outliers : 3.03 % Allowed : 28.36 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2507 helix: 0.62 (0.14), residues: 1401 sheet: -0.76 (0.60), residues: 73 loop : -1.38 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 719 HIS 0.007 0.001 HIS A 188 PHE 0.028 0.001 PHE A 160 TYR 0.042 0.002 TYR P 88 ARG 0.014 0.000 ARG U 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11803.11 seconds wall clock time: 213 minutes 50.51 seconds (12830.51 seconds total)