Starting phenix.real_space_refine on Wed Jul 24 21:39:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/07_2024/8kd3_37123_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/07_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_37123/07_2024/8kd3_37123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/07_2024/8kd3_37123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/07_2024/8kd3_37123_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kd3_37123/07_2024/8kd3_37123_neut.cif" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 12.18, per 1000 atoms: 0.44 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: 13.59 Conformation dependent library (CDL) restraints added in 3.5 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... Secondary structure from input PDB file: 103 helices and 18 sheets defined 56.7% alpha, 3.6% beta 139 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 10.99 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 removed outlier: 4.295A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET A 47 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.933A pdb=" N LYS A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 61 " --> pdb=" O TYR A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 61' Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 115 through 136 Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.574A pdb=" N LEU A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 removed outlier: 3.838A pdb=" N GLU A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 243 through 262 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 287 through 300 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 315 through 330 removed outlier: 3.564A pdb=" N ARG A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.569A pdb=" N TYR A 346 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 347 " --> pdb=" O TYR A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 347' Processing helix chain 'A' and resid 365 through 381 Processing helix chain 'B' and resid 665 through 677 removed outlier: 4.618A pdb=" N PHE B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLU B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 694 Processing helix chain 'B' and resid 698 through 710 removed outlier: 3.550A pdb=" N PHE B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 725 Processing helix chain 'B' and resid 759 through 764 removed outlier: 3.674A pdb=" N THR B 763 " --> pdb=" O PRO B 759 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 764 " --> pdb=" O LYS B 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 759 through 764' Processing helix chain 'B' and resid 771 through 778 Processing helix chain 'B' and resid 785 through 791 removed outlier: 3.711A pdb=" N ALA B 789 " --> pdb=" O HIS B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 839 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) Processing helix chain 'B' and resid 843 through 848 removed outlier: 4.023A pdb=" N ASN B 848 " --> pdb=" O ASN B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 872 through 886 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 890 through 929 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 934 through 943 removed outlier: 4.035A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 967 removed outlier: 3.808A pdb=" N ILE B 955 " --> pdb=" O GLU B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 997 removed outlier: 4.085A pdb=" N TYR B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 removed outlier: 3.632A pdb=" N ILE B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B1022 " --> pdb=" O ILE B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1164 removed outlier: 3.916A pdb=" N MET B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1174 removed outlier: 3.867A pdb=" N LYS B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1184 Processing helix chain 'B' and resid 1202 through 1217 Processing helix chain 'B' and resid 1221 through 1230 Processing helix chain 'B' and resid 1236 through 1240 removed outlier: 3.803A pdb=" N LEU B1239 " --> pdb=" O ALA B1236 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR B1240 " --> pdb=" O PHE B1237 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1236 through 1240' Processing helix chain 'B' and resid 1241 through 1259 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 1259 through 1273 Processing helix chain 'B' and resid 1282 through 1294 Processing helix chain 'B' and resid 1307 through 1309 No H-bonds generated for 'chain 'B' and resid 1307 through 1309' Processing helix chain 'D' and resid 98 through 113 Processing helix chain 'D' and resid 225 through 241 Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.587A pdb=" N LEU D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 293 Processing helix chain 'D' and resid 302 through 316 Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.517A pdb=" N ILE D 325 " --> pdb=" O PRO D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 344 removed outlier: 4.038A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 348 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 391 through 399 Processing helix chain 'E' and resid 292 through 296 removed outlier: 3.905A pdb=" N LEU E 296 " --> pdb=" O PRO E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 310 Processing helix chain 'E' and resid 321 through 330 removed outlier: 3.712A pdb=" N ILE E 327 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 345 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) removed outlier: 3.702A pdb=" N SER E 345 " --> pdb=" O PHE E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 360 removed outlier: 3.984A pdb=" N THR E 360 " --> pdb=" O TYR E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 387 Processing helix chain 'E' and resid 402 through 407 removed outlier: 3.566A pdb=" N THR E 405 " --> pdb=" O ASN E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 543 through 559 Processing helix chain 'F' and resid 98 through 113 removed outlier: 3.808A pdb=" N GLU F 102 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 239 removed outlier: 3.972A pdb=" N VAL F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) 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) Processing helix chain 'F' and resid 253 through 260 removed outlier: 4.371A pdb=" N VAL F 257 " --> pdb=" O THR F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 263 No H-bonds generated for 'chain 'F' and resid 261 through 263' Processing helix chain 'F' and resid 275 through 292 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 299 through 314 Processing helix chain 'F' and resid 328 through 338 removed outlier: 4.310A pdb=" N LEU F 332 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 348 through 368 removed outlier: 3.709A pdb=" N CYS F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET F 368 " --> pdb=" O VAL F 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 312 Processing helix chain 'G' and resid 321 through 329 removed outlier: 3.729A pdb=" N ASN G 325 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE G 327 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS G 328 " --> pdb=" O ASN G 325 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN G 329 " --> pdb=" O PHE G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 342 removed outlier: 3.828A pdb=" N PHE G 341 " --> pdb=" O ALA G 337 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN G 342 " --> pdb=" O LYS G 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 337 through 342' Processing helix chain 'G' and resid 541 through 570 removed outlier: 3.568A pdb=" N GLN G 570 " --> pdb=" O LEU G 566 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 57 removed outlier: 3.680A pdb=" N LYS O 56 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 77 removed outlier: 3.538A pdb=" N PHE O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 Processing helix chain 'P' and resid 25 through 29 removed outlier: 3.756A pdb=" N ILE P 29 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 3.929A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 92 removed outlier: 3.573A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 21 Processing helix chain 'Q' and resid 26 through 37 Processing helix chain 'Q' and resid 45 through 74 removed outlier: 4.346A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 removed outlier: 3.581A pdb=" N ASP Q 90 " --> pdb=" O ALA Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'R' and resid 34 through 46 Processing helix chain 'R' and resid 52 through 81 Processing helix chain 'R' and resid 87 through 99 removed outlier: 3.521A pdb=" N ILE R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 119 Processing helix chain 'S' and resid 44 through 56 removed outlier: 3.582A pdb=" N LYS S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 79 removed outlier: 3.757A pdb=" N PHE S 67 " --> pdb=" O ARG S 63 " (cutoff:3.500A) 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 85 through 114 Processing helix chain 'S' and resid 120 through 132 Processing helix chain 'T' and resid 24 through 29 removed outlier: 3.794A pdb=" N GLN T 27 " --> pdb=" O ASP T 24 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE T 29 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 41 Processing helix chain 'T' and resid 49 through 76 removed outlier: 3.790A pdb=" N GLU T 53 " --> pdb=" O LEU T 49 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 92 Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 26 through 36 Processing helix chain 'U' and resid 45 through 73 removed outlier: 4.179A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 90 removed outlier: 3.561A pdb=" N ASP U 90 " --> pdb=" O ALA U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 97 Processing helix chain 'V' and resid 34 through 46 Processing helix chain 'V' and resid 52 through 81 removed outlier: 3.782A pdb=" N ASN V 81 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 99 removed outlier: 3.511A pdb=" N ILE V 91 " --> pdb=" O THR V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 119 removed outlier: 4.023A pdb=" N LYS V 105 " --> pdb=" O GLY V 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 6.272A pdb=" N ALA A 142 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLY A 309 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ASN A 144 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N GLY A 311 " --> 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) removed outlier: 6.467A pdb=" N VAL A 180 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N CYS A 206 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TYR A 182 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N PHE A 208 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP A 184 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N LYS A 210 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL A 234 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL A 236 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER A 207 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU A 238 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS A 209 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 756 through 757 removed outlier: 4.156A pdb=" N LYS B 756 " --> pdb=" O VAL B 783 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 783 " --> pdb=" O LYS B 756 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 974 through 978 removed outlier: 5.070A pdb=" N LEU B 975 " --> pdb=" O ILE B1314 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B1314 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 977 " --> pdb=" O VAL B1312 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B1312 " --> pdb=" O PHE B 977 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AA5, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AA6, first strand: chain 'E' and resid 365 through 366 Processing sheet with id=AA7, first strand: chain 'E' and resid 437 through 439 Processing sheet with id=AA8, first strand: chain 'E' and resid 505 through 506 removed outlier: 6.833A pdb=" N TYR E 505 " --> pdb=" O ILE E 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 521 through 522 removed outlier: 5.704A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.905A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AB3, first strand: chain 'P' and resid 96 through 98 removed outlier: 6.212A pdb=" N THR P 96 " --> pdb=" O THR U 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.399A pdb=" N ARG Q 42 " --> pdb=" O ILE R 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'Q' and resid 77 through 78 Processing sheet with id=AB6, first strand: chain 'Q' and resid 100 through 102 Processing sheet with id=AB7, first strand: chain 'S' and resid 83 through 84 removed outlier: 7.190A pdb=" N ARG S 83 " --> pdb=" O VAL T 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'U' and resid 42 through 43 removed outlier: 7.028A pdb=" N ARG U 42 " --> pdb=" O ILE V 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'U' and resid 77 through 78 983 hydrogen bonds defined for protein. 2901 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: 14.88 Time building geometry restraints manager: 14.35 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: 1571 2.73 - 3.45: 38271 3.45 - 4.18: 72966 4.18 - 4.90: 117351 Nonbonded interactions: 230164 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 230159 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: 41.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 86.460 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.120 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:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.010 ------------------------------------------------------------------------------- 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= 0.270 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 : 2.536 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: 1.2583 time to fit residues: 489.0906 Evaluate side-chains 280 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 2.631 ------------------------------------------------------------------------------- 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: 0.6980 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: 1.9990 chunk 85 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 402 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 GLN G 302 HIS O 39 HIS P 25 ASN S 55 GLN S 85 GLN S 93 GLN V 60 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 28809 Z= 0.290 Angle : 0.615 11.457 40285 Z= 0.333 Chirality : 0.039 0.205 4442 Planarity : 0.004 0.067 3978 Dihedral : 26.408 175.002 6379 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.58 % Allowed : 25.20 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2507 helix: 0.44 (0.14), residues: 1388 sheet: 0.40 (0.58), residues: 98 loop : -1.56 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 365 HIS 0.007 0.001 HIS O 113 PHE 0.018 0.002 PHE A 215 TYR 0.023 0.002 TYR B1145 ARG 0.018 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 462 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 335 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8006 (ttp) REVERT: A 248 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7612 (mmm-85) REVERT: A 326 THR cc_start: 0.8887 (m) cc_final: 0.8645 (m) REVERT: A 373 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7100 (mpp) REVERT: B 1299 ASN cc_start: 0.6622 (OUTLIER) cc_final: 0.6386 (m-40) REVERT: D 309 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7518 (mt) REVERT: D 357 LYS cc_start: 0.8313 (tptt) cc_final: 0.7945 (ttmt) REVERT: D 368 MET cc_start: 0.7068 (mmm) cc_final: 0.6708 (mmp) REVERT: E 387 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.6098 (t80) REVERT: E 548 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8127 (ptpp) REVERT: F 244 LYS cc_start: 0.1919 (OUTLIER) cc_final: 0.0540 (tptt) REVERT: F 307 ASP cc_start: 0.4819 (t70) cc_final: 0.4581 (t70) REVERT: F 368 MET cc_start: 0.3688 (OUTLIER) cc_final: 0.2509 (ppp) REVERT: P 40 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7940 (ttp-170) REVERT: P 44 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8641 (tttt) REVERT: Q 90 ASP cc_start: 0.8336 (t0) cc_final: 0.8112 (t70) REVERT: R 45 VAL cc_start: 0.8501 (p) cc_final: 0.8229 (m) REVERT: R 53 SER cc_start: 0.9197 (p) cc_final: 0.8829 (m) REVERT: V 65 ASP cc_start: 0.8841 (t70) cc_final: 0.8619 (t70) outliers start: 127 outliers final: 37 residues processed: 412 average time/residue: 1.2917 time to fit residues: 623.6570 Evaluate side-chains 355 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 307 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 224 ILE 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 717 PHE Chi-restraints excluded: chain B residue 883 LEU 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 1003 SER 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 325 ILE Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 VAL 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 89 ASP 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 R residue 44 GLN 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 141 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 212 optimal weight: 0.6980 chunk 173 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 255 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 253 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN B 886 HIS F 317 GLN F 369 HIS G 302 HIS O 39 HIS ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 ASN U 73 ASN U 104 GLN V 60 ASN V 64 ASN V 81 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28809 Z= 0.260 Angle : 0.589 12.453 40285 Z= 0.320 Chirality : 0.038 0.252 4442 Planarity : 0.004 0.115 3978 Dihedral : 26.620 173.985 6379 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.83 % Allowed : 25.72 % Favored : 69.45 % 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: -0.21 (0.16), residues: 2507 helix: 0.76 (0.14), residues: 1384 sheet: 0.17 (0.57), residues: 94 loop : -1.41 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 775 HIS 0.006 0.001 HIS E 302 PHE 0.016 0.001 PHE A 85 TYR 0.025 0.002 TYR F 299 ARG 0.012 0.001 ARG U 71 *********************** 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 449 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 339 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6225 (p-80) REVERT: A 248 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7790 (mmm-85) REVERT: A 306 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8222 (ttp) REVERT: B 813 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7583 (mm-30) REVERT: D 109 LYS cc_start: 0.3628 (OUTLIER) cc_final: 0.2929 (ptmt) REVERT: D 317 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7481 (mm110) REVERT: D 357 LYS cc_start: 0.8373 (tptt) cc_final: 0.8100 (ttmt) REVERT: D 368 MET cc_start: 0.7387 (mmm) cc_final: 0.7063 (mmp) REVERT: E 350 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8858 (tt0) REVERT: E 371 GLN cc_start: 0.8736 (pm20) cc_final: 0.8364 (pm20) REVERT: E 522 ILE cc_start: 0.7614 (mm) cc_final: 0.7355 (mp) REVERT: E 557 LYS cc_start: 0.7600 (mmtt) cc_final: 0.7331 (pptt) REVERT: F 96 ARG cc_start: 0.1341 (OUTLIER) cc_final: -0.1598 (mmt180) REVERT: F 107 MET cc_start: 0.0381 (OUTLIER) cc_final: 0.0071 (ptt) REVERT: F 307 ASP cc_start: 0.4868 (t70) cc_final: 0.4618 (t70) REVERT: P 84 MET cc_start: 0.8938 (tpp) cc_final: 0.8687 (mmt) REVERT: Q 56 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8695 (tt0) REVERT: Q 90 ASP cc_start: 0.8332 (t0) cc_final: 0.8095 (t70) REVERT: R 53 SER cc_start: 0.9093 (p) cc_final: 0.8853 (m) REVERT: R 68 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7741 (mt-10) REVERT: T 27 GLN cc_start: 0.8721 (tp40) cc_final: 0.8491 (mm110) REVERT: U 90 ASP cc_start: 0.8179 (t70) cc_final: 0.7921 (t0) REVERT: V 68 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7774 (mp0) outliers start: 110 outliers final: 41 residues processed: 406 average time/residue: 1.3523 time to fit residues: 640.0429 Evaluate side-chains 357 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 307 time to evaluate : 2.518 ------------------------------------------------------------------------------- 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 224 ILE 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 689 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 350 GLN 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 452 VAL Chi-restraints excluded: chain E residue 474 VAL 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 107 MET Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 49 LEU 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 109 SER Chi-restraints excluded: chain S residue 45 THR 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 79 ILE Chi-restraints excluded: chain V residue 68 GLU 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: 4.9990 chunk 192 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 171 optimal weight: 0.0270 chunk 256 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN A 419 GLN B1230 GLN D 393 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 HIS ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN V 64 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 28809 Z= 0.330 Angle : 0.609 9.807 40285 Z= 0.330 Chirality : 0.039 0.199 4442 Planarity : 0.004 0.053 3978 Dihedral : 26.669 175.373 6379 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.58 % Allowed : 25.07 % 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: -0.19 (0.16), residues: 2507 helix: 0.79 (0.14), residues: 1392 sheet: -0.32 (0.55), residues: 93 loop : -1.38 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 775 HIS 0.008 0.001 HIS B 785 PHE 0.015 0.002 PHE E 272 TYR 0.022 0.002 TYR A 347 ARG 0.009 0.001 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 438 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 311 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8980 (mtm) cc_final: 0.8775 (mtp) REVERT: A 189 HIS cc_start: 0.7516 (OUTLIER) cc_final: 0.6578 (p-80) REVERT: A 224 ILE cc_start: 0.8741 (pp) cc_final: 0.8457 (pp) REVERT: A 248 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7993 (mtp-110) REVERT: A 298 VAL cc_start: 0.8971 (p) cc_final: 0.8765 (t) REVERT: A 306 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8348 (ttp) REVERT: A 367 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: A 381 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6529 (pp20) REVERT: B 1182 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7127 (mmtm) REVERT: D 107 MET cc_start: 0.6054 (ppp) cc_final: 0.5851 (pmm) REVERT: D 357 LYS cc_start: 0.8473 (tptt) cc_final: 0.8217 (ttmt) REVERT: D 368 MET cc_start: 0.7528 (mmm) cc_final: 0.7311 (mmp) REVERT: E 359 GLU cc_start: 0.7493 (pt0) cc_final: 0.7255 (pp20) REVERT: E 365 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8335 (pttm) REVERT: E 371 GLN cc_start: 0.8746 (pm20) cc_final: 0.8260 (pm20) REVERT: E 387 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.6646 (m-80) REVERT: F 96 ARG cc_start: 0.1537 (OUTLIER) cc_final: -0.1436 (mmt180) REVERT: F 107 MET cc_start: 0.0139 (OUTLIER) cc_final: -0.0398 (ptt) REVERT: F 288 TYR cc_start: 0.5128 (OUTLIER) cc_final: 0.4262 (t80) REVERT: F 307 ASP cc_start: 0.4943 (t70) cc_final: 0.4671 (t70) REVERT: F 368 MET cc_start: 0.3387 (OUTLIER) cc_final: 0.1847 (tpt) REVERT: P 40 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8218 (ttp-170) REVERT: P 50 ILE cc_start: 0.8676 (tt) cc_final: 0.8457 (tt) REVERT: P 84 MET cc_start: 0.8850 (tpp) cc_final: 0.8574 (mmt) REVERT: Q 56 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8687 (tt0) REVERT: Q 73 ASN cc_start: 0.8674 (t0) cc_final: 0.8471 (t0) REVERT: Q 90 ASP cc_start: 0.8365 (t0) cc_final: 0.8108 (t70) REVERT: R 83 ARG cc_start: 0.8221 (mtt90) cc_final: 0.7982 (mmt90) REVERT: S 109 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8726 (mp) REVERT: U 90 ASP cc_start: 0.8313 (t70) cc_final: 0.8033 (t0) REVERT: V 46 HIS cc_start: 0.8690 (OUTLIER) cc_final: 0.8474 (m170) REVERT: V 65 ASP cc_start: 0.8960 (t70) cc_final: 0.8690 (t0) REVERT: V 102 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7645 (mp0) outliers start: 127 outliers final: 48 residues processed: 402 average time/residue: 1.3805 time to fit residues: 645.1355 Evaluate side-chains 354 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 289 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 PHE 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 367 GLU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 883 LEU 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 945 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 1230 GLN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain E residue 47 ASP 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 365 LYS 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 F residue 89 ASP 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 293 LEU Chi-restraints excluded: chain F residue 367 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 40 ARG Chi-restraints excluded: chain P residue 49 LEU 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 84 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 S residue 109 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 75 LYS Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 102 GLU Chi-restraints excluded: chain V residue 108 VAL 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: 0.8980 chunk 154 optimal weight: 20.0000 chunk 3 optimal weight: 0.5980 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 231 optimal weight: 0.8980 chunk 187 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 243 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 517 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4862 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= 0.215 Angle : 0.557 13.644 40285 Z= 0.304 Chirality : 0.037 0.191 4442 Planarity : 0.004 0.052 3978 Dihedral : 26.602 173.970 6379 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.04 % Allowed : 26.56 % Favored : 69.40 % 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: -0.00 (0.17), residues: 2507 helix: 0.99 (0.14), residues: 1396 sheet: -0.79 (0.53), residues: 101 loop : -1.32 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 775 HIS 0.006 0.001 HIS B 815 PHE 0.017 0.001 PHE G 552 TYR 0.022 0.001 TYR F 299 ARG 0.009 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 398 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 306 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: A 88 ARG cc_start: 0.8373 (mtm110) cc_final: 0.8038 (mtm-85) REVERT: A 189 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.6412 (p-80) REVERT: A 248 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7911 (mmm-85) REVERT: A 367 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: B 821 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8374 (mp) REVERT: B 982 LYS cc_start: 0.7193 (mtmt) cc_final: 0.6922 (tttt) REVERT: B 1182 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7176 (mmtm) REVERT: B 1288 LEU cc_start: 0.7927 (mp) cc_final: 0.7646 (mm) REVERT: D 357 LYS cc_start: 0.8423 (tptt) cc_final: 0.8160 (ttmt) REVERT: E 359 GLU cc_start: 0.7518 (pt0) cc_final: 0.7306 (pp20) REVERT: E 365 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8272 (pttm) REVERT: E 371 GLN cc_start: 0.8741 (pm20) cc_final: 0.8237 (pm20) REVERT: E 387 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: E 557 LYS cc_start: 0.7311 (mmtt) cc_final: 0.7096 (pptt) REVERT: F 96 ARG cc_start: 0.1506 (OUTLIER) cc_final: -0.1454 (mmt180) REVERT: F 107 MET cc_start: 0.0163 (OUTLIER) cc_final: -0.0295 (ptt) REVERT: F 235 ASP cc_start: 0.5036 (OUTLIER) cc_final: 0.4792 (t0) REVERT: F 307 ASP cc_start: 0.5009 (t70) cc_final: 0.4749 (t70) REVERT: P 40 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8176 (ttp-170) REVERT: P 50 ILE cc_start: 0.8631 (tt) cc_final: 0.8422 (tt) REVERT: Q 56 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8678 (tt0) REVERT: Q 73 ASN cc_start: 0.8729 (t0) cc_final: 0.8419 (t0) REVERT: Q 90 ASP cc_start: 0.8318 (t0) cc_final: 0.8067 (t70) REVERT: R 68 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8005 (mm-30) REVERT: U 29 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.7521 (ttp80) REVERT: U 90 ASP cc_start: 0.8238 (t70) cc_final: 0.7972 (t0) REVERT: V 43 LYS cc_start: 0.8388 (mmtp) cc_final: 0.8185 (mmtp) outliers start: 92 outliers final: 39 residues processed: 367 average time/residue: 1.3694 time to fit residues: 587.0769 Evaluate side-chains 335 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 282 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 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 293 ASN 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 883 LEU 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 945 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 D residue 252 VAL Chi-restraints excluded: chain D residue 295 ASN 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 365 LYS 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 519 ASN 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 335 ILE Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 49 LEU 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 R residue 84 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 75 LYS 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: 0.6980 chunk 244 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 271 optimal weight: 1.9990 chunk 225 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN ** 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: 0.7236 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28809 Z= 0.257 Angle : 0.580 12.750 40285 Z= 0.316 Chirality : 0.038 0.215 4442 Planarity : 0.004 0.053 3978 Dihedral : 26.582 175.488 6379 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.21 % Allowed : 26.38 % Favored : 69.40 % 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: 0.01 (0.17), residues: 2507 helix: 1.00 (0.14), residues: 1399 sheet: -0.94 (0.53), residues: 101 loop : -1.30 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 719 HIS 0.006 0.001 HIS B 815 PHE 0.033 0.001 PHE G 308 TYR 0.026 0.002 TYR A 347 ARG 0.009 0.000 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 401 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 305 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.6631 (p-80) REVERT: A 248 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7679 (mmm-85) REVERT: A 306 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8139 (ttp) REVERT: A 367 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: A 380 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8762 (mp) REVERT: B 765 MET cc_start: 0.3956 (OUTLIER) cc_final: 0.3257 (tpp) REVERT: B 1182 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7033 (mppt) REVERT: B 1288 LEU cc_start: 0.8033 (mp) cc_final: 0.7812 (mp) REVERT: D 22 MET cc_start: 0.6736 (mtt) cc_final: 0.6240 (mpt) REVERT: D 107 MET cc_start: 0.7381 (pmm) cc_final: 0.6722 (pp-130) REVERT: D 357 LYS cc_start: 0.8450 (tptt) cc_final: 0.8189 (ttmt) REVERT: D 371 ASP cc_start: 0.7048 (t0) cc_final: 0.6799 (OUTLIER) REVERT: E 371 GLN cc_start: 0.8756 (pm20) cc_final: 0.8231 (pm20) REVERT: E 387 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.6635 (m-80) REVERT: F 96 ARG cc_start: 0.1452 (OUTLIER) cc_final: -0.1463 (mmt180) REVERT: F 107 MET cc_start: 0.0158 (OUTLIER) cc_final: -0.0294 (ptt) REVERT: F 307 ASP cc_start: 0.5074 (t70) cc_final: 0.4819 (t70) REVERT: F 368 MET cc_start: 0.2995 (pp-130) cc_final: 0.1576 (tpt) REVERT: P 40 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8628 (ttm170) REVERT: P 50 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8418 (tt) REVERT: Q 56 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8673 (tt0) REVERT: Q 73 ASN cc_start: 0.8745 (t0) cc_final: 0.8366 (t0) REVERT: Q 90 ASP cc_start: 0.8313 (t0) cc_final: 0.8079 (t70) REVERT: R 68 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8014 (mm-30) REVERT: U 29 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.7548 (ttp80) REVERT: U 75 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8736 (mmtm) REVERT: U 90 ASP cc_start: 0.8239 (t70) cc_final: 0.7960 (t0) REVERT: V 46 HIS cc_start: 0.8741 (OUTLIER) cc_final: 0.8433 (m170) REVERT: V 68 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7817 (mp0) outliers start: 96 outliers final: 44 residues processed: 366 average time/residue: 1.4790 time to fit residues: 628.2098 Evaluate side-chains 351 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 291 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 367 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 780 ASP 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 945 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 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 367 LEU 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 E residue 519 ASN Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 89 ASP 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 367 LEU 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 40 ARG Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 50 ILE 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 R residue 84 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 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 75 LYS Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 68 GLU 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: 0.9990 chunk 154 optimal weight: 20.0000 chunk 198 optimal weight: 0.9980 chunk 153 optimal weight: 8.9990 chunk 228 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 chunk 169 optimal weight: 30.0000 chunk 165 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 108 ASN T 25 ASN V 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 28809 Z= 0.486 Angle : 0.689 13.662 40285 Z= 0.372 Chirality : 0.044 0.265 4442 Planarity : 0.005 0.088 3978 Dihedral : 27.058 175.755 6379 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.95 % Favored : 95.01 % Rotamer: Outliers : 4.13 % Allowed : 26.56 % Favored : 69.32 % 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: -0.38 (0.16), residues: 2507 helix: 0.61 (0.14), residues: 1407 sheet: -1.28 (0.53), residues: 91 loop : -1.35 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 719 HIS 0.009 0.001 HIS B 815 PHE 0.029 0.002 PHE A 160 TYR 0.036 0.002 TYR P 88 ARG 0.014 0.001 ARG V 89 *********************** 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 398 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 304 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7175 (mttm) cc_final: 0.6718 (mtpp) REVERT: A 97 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6255 (t80) REVERT: A 189 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.7060 (p-80) REVERT: A 248 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7939 (mmm-85) REVERT: A 261 TRP cc_start: 0.7909 (m-10) cc_final: 0.7379 (m-90) REVERT: A 306 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8448 (ttp) REVERT: A 367 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: A 422 ARG cc_start: 0.5331 (OUTLIER) cc_final: 0.4288 (ttt-90) REVERT: B 765 MET cc_start: 0.4546 (OUTLIER) cc_final: 0.4268 (tpt) REVERT: B 1264 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7322 (mt-10) REVERT: B 1288 LEU cc_start: 0.8181 (mp) cc_final: 0.7971 (mp) REVERT: D 22 MET cc_start: 0.6621 (mtt) cc_final: 0.6177 (mpt) REVERT: D 107 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6799 (pp-130) REVERT: D 357 LYS cc_start: 0.8511 (tptt) cc_final: 0.8293 (ttmt) REVERT: D 372 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6948 (pm20) REVERT: D 395 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7905 (tm-30) REVERT: E 538 LYS cc_start: 0.6358 (OUTLIER) cc_final: 0.6147 (ttmt) REVERT: F 96 ARG cc_start: 0.1598 (OUTLIER) cc_final: -0.1327 (mmt180) REVERT: F 107 MET cc_start: 0.0116 (OUTLIER) cc_final: -0.0399 (ptt) REVERT: F 288 TYR cc_start: 0.5187 (OUTLIER) cc_final: 0.3939 (t80) REVERT: F 307 ASP cc_start: 0.5094 (t70) cc_final: 0.4787 (t70) REVERT: F 368 MET cc_start: 0.3131 (OUTLIER) cc_final: 0.1662 (tpt) REVERT: Q 56 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8726 (tt0) REVERT: Q 73 ASN cc_start: 0.8677 (t0) cc_final: 0.8330 (t0) REVERT: Q 90 ASP cc_start: 0.8406 (t0) cc_final: 0.8149 (t70) REVERT: R 44 GLN cc_start: 0.8811 (tt0) cc_final: 0.8586 (tt0) REVERT: R 68 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8035 (mm-30) REVERT: R 76 ARG cc_start: 0.8481 (ttm-80) cc_final: 0.8163 (ttm110) REVERT: S 87 SER cc_start: 0.9292 (t) cc_final: 0.9049 (p) REVERT: S 109 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8997 (mp) REVERT: T 77 LYS cc_start: 0.8431 (mmtt) cc_final: 0.8209 (mmpt) REVERT: U 29 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.7639 (ttp80) REVERT: U 64 GLU cc_start: 0.8259 (tt0) cc_final: 0.7911 (tp30) REVERT: U 75 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8796 (mmtm) REVERT: U 90 ASP cc_start: 0.8341 (t70) cc_final: 0.8045 (t0) outliers start: 94 outliers final: 42 residues processed: 366 average time/residue: 1.4157 time to fit residues: 602.3748 Evaluate side-chains 349 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 289 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 306 MET 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 A residue 422 ARG Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 780 ASP Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 47 ASP 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 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 E residue 538 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 288 TYR Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 368 MET 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 62 ILE 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 57 SER Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 109 LEU 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 75 LYS Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 167 optimal weight: 8.9990 chunk 108 optimal weight: 0.5980 chunk 161 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 184 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 212 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 379 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 798 HIS ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN D 295 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN T 25 ASN V 46 HIS V 64 ASN V 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28809 Z= 0.196 Angle : 0.577 11.238 40285 Z= 0.316 Chirality : 0.037 0.184 4442 Planarity : 0.004 0.054 3978 Dihedral : 26.832 174.013 6379 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 3.38 % Allowed : 27.17 % Favored : 69.45 % 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: -0.08 (0.17), residues: 2507 helix: 0.90 (0.14), residues: 1407 sheet: -0.73 (0.62), residues: 73 loop : -1.33 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 719 HIS 0.005 0.001 HIS B 785 PHE 0.022 0.001 PHE G 308 TYR 0.041 0.001 TYR P 88 ARG 0.010 0.000 ARG D 324 *********************** 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 390 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 313 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7015 (mttm) cc_final: 0.6585 (mtpp) REVERT: A 97 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.5949 (t80) REVERT: A 189 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.6824 (p-80) REVERT: A 211 TYR cc_start: 0.7760 (t80) cc_final: 0.7490 (t80) REVERT: A 248 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7909 (mmm-85) REVERT: A 367 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: B 1160 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7695 (mp0) REVERT: B 1264 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6842 (mp0) REVERT: D 22 MET cc_start: 0.6599 (mtt) cc_final: 0.6156 (mpt) REVERT: D 107 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.6803 (pp-130) REVERT: D 357 LYS cc_start: 0.8450 (tptt) cc_final: 0.8205 (ttmt) REVERT: E 371 GLN cc_start: 0.8829 (pm20) cc_final: 0.8247 (pm20) REVERT: E 386 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7866 (tt) REVERT: E 387 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: F 96 ARG cc_start: 0.1607 (OUTLIER) cc_final: -0.1320 (mmt180) REVERT: F 107 MET cc_start: 0.0175 (OUTLIER) cc_final: -0.0290 (ptt) REVERT: F 288 TYR cc_start: 0.5208 (OUTLIER) cc_final: 0.4088 (t80) REVERT: F 307 ASP cc_start: 0.5063 (t70) cc_final: 0.4749 (t70) REVERT: F 368 MET cc_start: 0.3041 (OUTLIER) cc_final: 0.1605 (tpt) REVERT: P 50 ILE cc_start: 0.8470 (tt) cc_final: 0.8261 (tt) REVERT: Q 56 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8647 (tt0) REVERT: Q 73 ASN cc_start: 0.8644 (t0) cc_final: 0.8299 (t0) REVERT: Q 90 ASP cc_start: 0.8329 (t0) cc_final: 0.8072 (t70) REVERT: R 44 GLN cc_start: 0.8689 (tt0) cc_final: 0.8428 (tt0) REVERT: R 68 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7977 (mm-30) REVERT: R 76 ARG cc_start: 0.8309 (ttm-80) cc_final: 0.8053 (ttm110) REVERT: S 109 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8688 (mp) REVERT: U 29 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.7598 (ttp80) REVERT: U 90 ASP cc_start: 0.8208 (t70) cc_final: 0.7944 (t0) REVERT: V 49 THR cc_start: 0.7901 (t) cc_final: 0.7559 (t) REVERT: V 90 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8313 (mp0) outliers start: 77 outliers final: 31 residues processed: 363 average time/residue: 1.3825 time to fit residues: 588.9931 Evaluate side-chains 340 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 294 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 945 THR Chi-restraints excluded: chain D residue 107 MET 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 364 VAL Chi-restraints excluded: chain E residue 386 LEU 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 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 368 MET 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 62 ILE 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 109 LEU 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 V residue 81 ASN Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 246 optimal weight: 0.7980 chunk 259 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 198 optimal weight: 0.5980 chunk 77 optimal weight: 10.0000 chunk 228 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN D 295 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.6062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 28809 Z= 0.299 Angle : 0.620 14.318 40285 Z= 0.333 Chirality : 0.039 0.204 4442 Planarity : 0.004 0.058 3978 Dihedral : 26.838 175.996 6379 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.87 % Favored : 95.09 % Rotamer: Outliers : 3.07 % Allowed : 27.48 % Favored : 69.45 % 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: -0.12 (0.17), residues: 2507 helix: 0.88 (0.14), residues: 1408 sheet: -1.13 (0.58), residues: 81 loop : -1.33 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 719 HIS 0.006 0.001 HIS O 39 PHE 0.029 0.002 PHE A 160 TYR 0.046 0.002 TYR P 88 ARG 0.010 0.000 ARG D 324 *********************** 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 368 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 298 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6078 (t80) REVERT: A 189 HIS cc_start: 0.7845 (OUTLIER) cc_final: 0.6934 (p-80) REVERT: A 248 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7915 (mmm-85) REVERT: A 261 TRP cc_start: 0.7837 (m-10) cc_final: 0.7274 (m-90) REVERT: A 306 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8143 (ttp) REVERT: A 367 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: B 700 ASP cc_start: 0.8545 (m-30) cc_final: 0.8287 (m-30) REVERT: B 1160 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7694 (mp0) REVERT: D 22 MET cc_start: 0.6581 (mtt) cc_final: 0.6139 (mpt) REVERT: D 107 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6765 (pp-130) REVERT: D 357 LYS cc_start: 0.8463 (tptt) cc_final: 0.8223 (ttmt) REVERT: E 371 GLN cc_start: 0.8863 (pm20) cc_final: 0.8287 (pm20) REVERT: E 522 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8503 (mm) REVERT: F 96 ARG cc_start: 0.1649 (OUTLIER) cc_final: -0.1280 (mmt180) REVERT: F 107 MET cc_start: 0.0109 (OUTLIER) cc_final: -0.0380 (ptt) REVERT: F 307 ASP cc_start: 0.5168 (t70) cc_final: 0.4874 (t70) REVERT: F 368 MET cc_start: 0.3086 (OUTLIER) cc_final: 0.1730 (tpt) REVERT: P 50 ILE cc_start: 0.8703 (tt) cc_final: 0.8470 (tt) REVERT: Q 56 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8686 (tt0) REVERT: Q 73 ASN cc_start: 0.8655 (t0) cc_final: 0.8313 (t0) REVERT: Q 90 ASP cc_start: 0.8330 (t0) cc_final: 0.8084 (t70) REVERT: R 44 GLN cc_start: 0.8767 (tt0) cc_final: 0.8485 (tt0) REVERT: R 68 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8047 (mm-30) REVERT: R 73 GLU cc_start: 0.8786 (tp30) cc_final: 0.8577 (tp30) REVERT: R 76 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.8086 (ttm110) REVERT: S 109 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8714 (mp) REVERT: U 90 ASP cc_start: 0.8221 (t70) cc_final: 0.7953 (t0) outliers start: 70 outliers final: 35 residues processed: 349 average time/residue: 1.4015 time to fit residues: 568.9030 Evaluate side-chains 335 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 288 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 306 MET 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 889 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain D residue 107 MET 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 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 395 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 522 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 368 MET Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 557 LYS 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 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 S residue 57 SER Chi-restraints excluded: chain S residue 109 LEU 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 V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 165 optimal weight: 8.9990 chunk 266 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 279 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 222 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 172 optimal weight: 0.0030 chunk 136 optimal weight: 3.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN D 295 ASN ** E 519 ASN ** 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 46 HIS V 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.6128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28809 Z= 0.270 Angle : 0.619 13.698 40285 Z= 0.330 Chirality : 0.038 0.197 4442 Planarity : 0.004 0.057 3978 Dihedral : 26.832 174.493 6379 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.79 % Favored : 95.17 % Rotamer: Outliers : 2.81 % Allowed : 28.09 % Favored : 69.10 % 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: -0.08 (0.17), residues: 2507 helix: 0.89 (0.14), residues: 1408 sheet: -0.70 (0.61), residues: 73 loop : -1.32 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 719 HIS 0.005 0.001 HIS B 815 PHE 0.028 0.002 PHE A 160 TYR 0.049 0.002 TYR P 88 ARG 0.014 0.001 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 363 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 299 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6041 (t80) REVERT: A 189 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.6885 (p-80) REVERT: A 224 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8319 (pp) REVERT: A 248 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7918 (mmm-85) REVERT: A 261 TRP cc_start: 0.7848 (m-10) cc_final: 0.7270 (m-90) REVERT: A 306 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8095 (ttp) REVERT: A 367 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: A 380 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8726 (mp) REVERT: B 700 ASP cc_start: 0.8542 (m-30) cc_final: 0.8287 (m-30) REVERT: B 1160 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7673 (mp0) REVERT: D 22 MET cc_start: 0.6546 (mtt) cc_final: 0.6113 (mpt) REVERT: D 107 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6762 (pp-130) REVERT: D 357 LYS cc_start: 0.8448 (tptt) cc_final: 0.8215 (ttmt) REVERT: E 359 GLU cc_start: 0.7935 (pp20) cc_final: 0.7643 (pp20) REVERT: E 371 GLN cc_start: 0.8883 (pm20) cc_final: 0.8333 (pm20) REVERT: E 387 PHE cc_start: 0.6974 (OUTLIER) cc_final: 0.6494 (m-80) REVERT: E 522 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8504 (mm) REVERT: F 96 ARG cc_start: 0.1564 (OUTLIER) cc_final: -0.1254 (mmt180) REVERT: F 107 MET cc_start: 0.0073 (OUTLIER) cc_final: -0.0423 (ptt) REVERT: F 235 ASP cc_start: 0.5101 (OUTLIER) cc_final: 0.4821 (t0) REVERT: F 307 ASP cc_start: 0.5094 (t70) cc_final: 0.4805 (t70) REVERT: F 368 MET cc_start: 0.3138 (OUTLIER) cc_final: 0.1754 (tpt) REVERT: P 50 ILE cc_start: 0.8633 (tt) cc_final: 0.8430 (tt) REVERT: Q 56 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8674 (tt0) REVERT: Q 73 ASN cc_start: 0.8650 (t0) cc_final: 0.8283 (t0) REVERT: Q 90 ASP cc_start: 0.8330 (t0) cc_final: 0.8095 (t70) REVERT: R 44 GLN cc_start: 0.8744 (tt0) cc_final: 0.8469 (tt0) REVERT: R 68 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8056 (mm-30) REVERT: R 76 ARG cc_start: 0.8334 (ttm-80) cc_final: 0.8066 (ttm110) REVERT: S 109 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8703 (mp) REVERT: U 90 ASP cc_start: 0.8212 (t70) cc_final: 0.7945 (t0) outliers start: 64 outliers final: 32 residues processed: 344 average time/residue: 1.3989 time to fit residues: 562.9630 Evaluate side-chains 333 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 285 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 306 MET 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 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 945 THR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain D residue 107 MET 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 274 CYS 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 522 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 235 ASP Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 368 MET 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 62 ILE Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain S residue 109 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 V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 177 optimal weight: 5.9990 chunk 237 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 229 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN D 295 ASN ** E 519 ASN ** 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 46 HIS V 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.126118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.094044 restraints weight = 54988.747| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.74 r_work: 0.3166 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28809 Z= 0.236 Angle : 0.605 14.356 40285 Z= 0.324 Chirality : 0.038 0.184 4442 Planarity : 0.004 0.054 3978 Dihedral : 26.764 174.751 6379 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.91 % Favored : 95.05 % Rotamer: Outliers : 2.68 % Allowed : 28.45 % Favored : 68.88 % 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: -0.01 (0.17), residues: 2507 helix: 0.96 (0.14), residues: 1406 sheet: -0.66 (0.61), residues: 73 loop : -1.30 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 719 HIS 0.005 0.001 HIS O 39 PHE 0.026 0.001 PHE A 160 TYR 0.051 0.002 TYR P 88 ARG 0.013 0.001 ARG U 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11078.75 seconds wall clock time: 195 minutes 39.45 seconds (11739.45 seconds total)