Starting phenix.real_space_refine on Tue Feb 20 18:21:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ets_28597/02_2024/8ets_28597_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ets_28597/02_2024/8ets_28597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ets_28597/02_2024/8ets_28597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ets_28597/02_2024/8ets_28597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ets_28597/02_2024/8ets_28597_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ets_28597/02_2024/8ets_28597_updated.pdb" } resolution = 3.04 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= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 95 5.16 5 C 18041 2.51 5 N 4942 2.21 5 O 5580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q ASP 1021": "OD1" <-> "OD2" Residue "Q GLU 1154": "OE1" <-> "OE2" Residue "Q PHE 1167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 1222": "OE1" <-> "OE2" Residue "Q GLU 1276": "OE1" <-> "OE2" Residue "Q PHE 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 1333": "OE1" <-> "OE2" Residue "Q TYR 1334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 1393": "OD1" <-> "OD2" Residue "R TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 259": "OE1" <-> "OE2" Residue "R GLU 262": "OE1" <-> "OE2" Residue "R GLU 268": "OE1" <-> "OE2" Residue "R GLU 687": "OE1" <-> "OE2" Residue "R GLU 722": "OE1" <-> "OE2" Residue "R TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 28": "OE1" <-> "OE2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "S PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 69": "OD1" <-> "OD2" Residue "S GLU 104": "OE1" <-> "OE2" Residue "S GLU 138": "OE1" <-> "OE2" Residue "S GLU 154": "OE1" <-> "OE2" Residue "T GLU 119": "OE1" <-> "OE2" Residue "T TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 216": "OD1" <-> "OD2" Residue "T GLU 227": "OE1" <-> "OE2" Residue "T ASP 311": "OD1" <-> "OD2" Residue "T GLU 312": "OE1" <-> "OE2" Residue "T ASP 352": "OD1" <-> "OD2" Residue "U ASP 95": "OD1" <-> "OD2" Residue "U GLU 110": "OE1" <-> "OE2" Residue "U GLU 134": "OE1" <-> "OE2" Residue "U GLU 170": "OE1" <-> "OE2" Residue "U ASP 188": "OD1" <-> "OD2" Residue "U GLU 226": "OE1" <-> "OE2" Residue "U GLU 228": "OE1" <-> "OE2" Residue "U ASP 245": "OD1" <-> "OD2" Residue "U ASP 271": "OD1" <-> "OD2" Residue "U GLU 279": "OE1" <-> "OE2" Residue "U GLU 287": "OE1" <-> "OE2" Residue "U GLU 316": "OE1" <-> "OE2" Residue "U TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 346": "OD1" <-> "OD2" Residue "U GLU 376": "OE1" <-> "OE2" Residue "U ASP 382": "OD1" <-> "OD2" Residue "U ASP 385": "OD1" <-> "OD2" Residue "U ASP 422": "OD1" <-> "OD2" Residue "U TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 192": "OE1" <-> "OE2" Residue "V GLU 227": "OE1" <-> "OE2" Residue "V ASP 253": "OD1" <-> "OD2" Residue "V GLU 282": "OE1" <-> "OE2" Residue "V GLU 302": "OE1" <-> "OE2" Residue "V GLU 351": "OE1" <-> "OE2" Residue "V GLU 441": "OE1" <-> "OE2" Residue "V TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 42": "OE1" <-> "OE2" Residue "W ASP 95": "OD1" <-> "OD2" Residue "W ASP 213": "OD1" <-> "OD2" Residue "W GLU 228": "OE1" <-> "OE2" Residue "W ASP 261": "OD1" <-> "OD2" Residue "W GLU 283": "OE1" <-> "OE2" Residue "W GLU 316": "OE1" <-> "OE2" Residue "W GLU 374": "OE1" <-> "OE2" Residue "W ASP 382": "OD1" <-> "OD2" Residue "X TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 187": "OE1" <-> "OE2" Residue "X ASP 216": "OD1" <-> "OD2" Residue "X GLU 225": "OE1" <-> "OE2" Residue "X GLU 227": "OE1" <-> "OE2" Residue "X ASP 246": "OD1" <-> "OD2" Residue "X ASP 251": "OD1" <-> "OD2" Residue "X ASP 253": "OD1" <-> "OD2" Residue "X ASP 311": "OD1" <-> "OD2" Residue "X GLU 312": "OE1" <-> "OE2" Residue "Y GLU 33": "OE1" <-> "OE2" Residue "Y ASP 95": "OD1" <-> "OD2" Residue "Y GLU 131": "OE1" <-> "OE2" Residue "Y ASP 213": "OD1" <-> "OD2" Residue "Y GLU 243": "OE1" <-> "OE2" Residue "Y ASP 261": "OD1" <-> "OD2" Residue "Y GLU 268": "OE1" <-> "OE2" Residue "Y ASP 302": "OD1" <-> "OD2" Residue "Y GLU 374": "OE1" <-> "OE2" Residue "Y GLU 376": "OE1" <-> "OE2" Residue "Y PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 303": "OE1" <-> "OE2" Residue "Z GLU 313": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28670 Number of models: 1 Model: "" Number of chains: 16 Chain: "Q" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3385 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 22, 'TRANS': 395} Chain breaks: 5 Chain: "R" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3548 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain breaks: 1 Chain: "S" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1014 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 9, 'TRANS': 115} Chain breaks: 1 Chain: "T" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3339 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3354 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3404 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "W" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3398 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 431} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "Y" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3421 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 434} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 248 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.21, per 1000 atoms: 0.53 Number of scatterers: 28670 At special positions: 0 Unit cell: (161.155, 150.3, 177.855, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 95 16.00 P 12 15.00 O 5580 8.00 N 4942 7.00 C 18041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.58 Conformation dependent library (CDL) restraints added in 4.8 seconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6820 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 152 helices and 30 sheets defined 38.0% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.80 Creating SS restraints... Processing helix chain 'Q' and resid 958 through 970 Processing helix chain 'Q' and resid 975 through 984 Processing helix chain 'Q' and resid 1000 through 1012 removed outlier: 4.028A pdb=" N GLN Q1006 " --> pdb=" O ASN Q1002 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE Q1007 " --> pdb=" O ALA Q1003 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1014 through 1017 No H-bonds generated for 'chain 'Q' and resid 1014 through 1017' Processing helix chain 'Q' and resid 1087 through 1093 Processing helix chain 'Q' and resid 1102 through 1110 Processing helix chain 'Q' and resid 1122 through 1132 Processing helix chain 'Q' and resid 1139 through 1145 removed outlier: 3.647A pdb=" N THR Q1145 " --> pdb=" O PHE Q1141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1148 through 1153 Processing helix chain 'Q' and resid 1170 through 1179 removed outlier: 3.770A pdb=" N VAL Q1177 " --> pdb=" O GLU Q1173 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR Q1178 " --> pdb=" O LEU Q1174 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG Q1179 " --> pdb=" O LEU Q1175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1186 through 1191 Processing helix chain 'Q' and resid 1193 through 1200 Processing helix chain 'Q' and resid 1203 through 1205 No H-bonds generated for 'chain 'Q' and resid 1203 through 1205' Processing helix chain 'Q' and resid 1227 through 1237 Processing helix chain 'Q' and resid 1240 through 1245 Processing helix chain 'Q' and resid 1251 through 1258 Processing helix chain 'Q' and resid 1265 through 1267 No H-bonds generated for 'chain 'Q' and resid 1265 through 1267' Processing helix chain 'Q' and resid 1293 through 1296 No H-bonds generated for 'chain 'Q' and resid 1293 through 1296' Processing helix chain 'Q' and resid 1299 through 1314 removed outlier: 3.919A pdb=" N VAL Q1309 " --> pdb=" O ASP Q1305 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS Q1310 " --> pdb=" O GLU Q1306 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU Q1311 " --> pdb=" O LEU Q1307 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1326 through 1338 Processing helix chain 'Q' and resid 1357 through 1363 Processing helix chain 'Q' and resid 1398 through 1407 removed outlier: 4.327A pdb=" N GLN Q1403 " --> pdb=" O THR Q1399 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1428 through 1431 No H-bonds generated for 'chain 'Q' and resid 1428 through 1431' Processing helix chain 'R' and resid 31 through 33 No H-bonds generated for 'chain 'R' and resid 31 through 33' Processing helix chain 'R' and resid 83 through 86 Processing helix chain 'R' and resid 90 through 94 Processing helix chain 'R' and resid 109 through 121 Processing helix chain 'R' and resid 144 through 157 removed outlier: 3.977A pdb=" N GLU R 156 " --> pdb=" O GLN R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 176 Processing helix chain 'R' and resid 216 through 230 Processing helix chain 'R' and resid 240 through 249 Processing helix chain 'R' and resid 257 through 260 No H-bonds generated for 'chain 'R' and resid 257 through 260' Processing helix chain 'R' and resid 267 through 270 No H-bonds generated for 'chain 'R' and resid 267 through 270' Processing helix chain 'R' and resid 586 through 588 No H-bonds generated for 'chain 'R' and resid 586 through 588' Processing helix chain 'R' and resid 590 through 596 Processing helix chain 'R' and resid 608 through 610 No H-bonds generated for 'chain 'R' and resid 608 through 610' Processing helix chain 'R' and resid 617 through 620 No H-bonds generated for 'chain 'R' and resid 617 through 620' Processing helix chain 'R' and resid 622 through 625 removed outlier: 3.979A pdb=" N ILE R 625 " --> pdb=" O PRO R 622 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 622 through 625' Processing helix chain 'R' and resid 628 through 630 No H-bonds generated for 'chain 'R' and resid 628 through 630' Processing helix chain 'R' and resid 638 through 648 Processing helix chain 'R' and resid 659 through 667 removed outlier: 3.613A pdb=" N ASN R 667 " --> pdb=" O ASP R 663 " (cutoff:3.500A) Processing helix chain 'R' and resid 680 through 691 Processing helix chain 'R' and resid 709 through 719 Processing helix chain 'R' and resid 731 through 737 Processing helix chain 'S' and resid 32 through 39 removed outlier: 3.723A pdb=" N VAL S 36 " --> pdb=" O PHE S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 82 removed outlier: 4.129A pdb=" N ILE S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 103 No H-bonds generated for 'chain 'S' and resid 100 through 103' Processing helix chain 'S' and resid 137 through 143 Processing helix chain 'S' and resid 151 through 156 Processing helix chain 'T' and resid 52 through 67 Processing helix chain 'T' and resid 85 through 96 Processing helix chain 'T' and resid 107 through 110 removed outlier: 3.704A pdb=" N LEU T 110 " --> pdb=" O GLY T 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 107 through 110' Processing helix chain 'T' and resid 117 through 128 removed outlier: 4.102A pdb=" N ALA T 128 " --> pdb=" O ASN T 124 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 191 Processing helix chain 'T' and resid 216 through 218 No H-bonds generated for 'chain 'T' and resid 216 through 218' Processing helix chain 'T' and resid 249 through 256 Processing helix chain 'T' and resid 282 through 297 Processing helix chain 'T' and resid 313 through 315 No H-bonds generated for 'chain 'T' and resid 313 through 315' Processing helix chain 'T' and resid 318 through 329 removed outlier: 3.864A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU T 329 " --> pdb=" O ASN T 325 " (cutoff:3.500A) Processing helix chain 'T' and resid 356 through 358 No H-bonds generated for 'chain 'T' and resid 356 through 358' Processing helix chain 'T' and resid 361 through 364 No H-bonds generated for 'chain 'T' and resid 361 through 364' Processing helix chain 'T' and resid 377 through 390 Processing helix chain 'T' and resid 397 through 409 Processing helix chain 'T' and resid 412 through 428 removed outlier: 3.635A pdb=" N LEU T 416 " --> pdb=" O LEU T 412 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix Processing helix chain 'T' and resid 436 through 445 Processing helix chain 'T' and resid 449 through 457 Processing helix chain 'U' and resid 48 through 63 Processing helix chain 'U' and resid 81 through 92 Processing helix chain 'U' and resid 113 through 124 removed outlier: 3.879A pdb=" N SER U 124 " --> pdb=" O ALA U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 180 Processing helix chain 'U' and resid 241 through 248 Processing helix chain 'U' and resid 254 through 259 removed outlier: 3.987A pdb=" N THR U 259 " --> pdb=" O ALA U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 267 through 283 Processing helix chain 'U' and resid 298 through 300 No H-bonds generated for 'chain 'U' and resid 298 through 300' Processing helix chain 'U' and resid 303 through 311 removed outlier: 3.572A pdb=" N ARG U 311 " --> pdb=" O SER U 307 " (cutoff:3.500A) Processing helix chain 'U' and resid 340 through 342 No H-bonds generated for 'chain 'U' and resid 340 through 342' Processing helix chain 'U' and resid 345 through 350 removed outlier: 3.808A pdb=" N ARG U 350 " --> pdb=" O ASP U 346 " (cutoff:3.500A) Processing helix chain 'U' and resid 361 through 374 Processing helix chain 'U' and resid 381 through 393 Processing helix chain 'U' and resid 396 through 412 removed outlier: 4.554A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE U 409 " --> pdb=" O VAL U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 420 through 429 Processing helix chain 'U' and resid 433 through 441 Processing helix chain 'U' and resid 444 through 446 No H-bonds generated for 'chain 'U' and resid 444 through 446' Processing helix chain 'V' and resid 52 through 67 Processing helix chain 'V' and resid 85 through 96 Processing helix chain 'V' and resid 107 through 110 removed outlier: 4.016A pdb=" N LEU V 110 " --> pdb=" O GLY V 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 107 through 110' Processing helix chain 'V' and resid 117 through 127 Processing helix chain 'V' and resid 183 through 191 removed outlier: 3.644A pdb=" N SER V 188 " --> pdb=" O THR V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 249 through 257 Processing helix chain 'V' and resid 265 through 270 Processing helix chain 'V' and resid 282 through 297 Processing helix chain 'V' and resid 313 through 315 No H-bonds generated for 'chain 'V' and resid 313 through 315' Processing helix chain 'V' and resid 318 through 329 removed outlier: 3.757A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU V 329 " --> pdb=" O ASN V 325 " (cutoff:3.500A) Processing helix chain 'V' and resid 356 through 358 No H-bonds generated for 'chain 'V' and resid 356 through 358' Processing helix chain 'V' and resid 361 through 364 No H-bonds generated for 'chain 'V' and resid 361 through 364' Processing helix chain 'V' and resid 377 through 390 Processing helix chain 'V' and resid 397 through 409 Processing helix chain 'V' and resid 412 through 416 Processing helix chain 'V' and resid 419 through 429 removed outlier: 3.729A pdb=" N SER V 429 " --> pdb=" O LEU V 425 " (cutoff:3.500A) Processing helix chain 'V' and resid 436 through 445 Processing helix chain 'V' and resid 449 through 457 Processing helix chain 'W' and resid 48 through 63 Processing helix chain 'W' and resid 81 through 91 Processing helix chain 'W' and resid 113 through 124 removed outlier: 4.078A pdb=" N SER W 124 " --> pdb=" O ALA W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 173 through 180 Processing helix chain 'W' and resid 241 through 249 Processing helix chain 'W' and resid 253 through 259 removed outlier: 3.915A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 267 through 282 Processing helix chain 'W' and resid 303 through 312 removed outlier: 3.798A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) Processing helix chain 'W' and resid 340 through 342 No H-bonds generated for 'chain 'W' and resid 340 through 342' Processing helix chain 'W' and resid 345 through 349 Processing helix chain 'W' and resid 361 through 374 Processing helix chain 'W' and resid 381 through 393 Processing helix chain 'W' and resid 396 through 412 removed outlier: 4.000A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS W 412 " --> pdb=" O GLN W 408 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 429 Processing helix chain 'W' and resid 433 through 441 Processing helix chain 'X' and resid 52 through 67 Processing helix chain 'X' and resid 85 through 96 Processing helix chain 'X' and resid 107 through 110 removed outlier: 3.862A pdb=" N LEU X 110 " --> pdb=" O GLY X 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 107 through 110' Processing helix chain 'X' and resid 117 through 128 removed outlier: 3.997A pdb=" N ALA X 128 " --> pdb=" O ASN X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 183 through 192 removed outlier: 3.519A pdb=" N GLU X 187 " --> pdb=" O THR X 184 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG X 191 " --> pdb=" O SER X 188 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU X 192 " --> pdb=" O ILE X 189 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 218 No H-bonds generated for 'chain 'X' and resid 216 through 218' Processing helix chain 'X' and resid 249 through 257 Processing helix chain 'X' and resid 265 through 271 Processing helix chain 'X' and resid 282 through 297 Processing helix chain 'X' and resid 313 through 315 No H-bonds generated for 'chain 'X' and resid 313 through 315' Processing helix chain 'X' and resid 318 through 329 removed outlier: 4.354A pdb=" N GLU X 329 " --> pdb=" O ASN X 325 " (cutoff:3.500A) Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 361 through 366 removed outlier: 4.110A pdb=" N ARG X 366 " --> pdb=" O ASP X 362 " (cutoff:3.500A) Processing helix chain 'X' and resid 377 through 390 Processing helix chain 'X' and resid 397 through 409 Processing helix chain 'X' and resid 412 through 417 Processing helix chain 'X' and resid 420 through 428 Processing helix chain 'X' and resid 436 through 445 Processing helix chain 'X' and resid 449 through 457 Processing helix chain 'Y' and resid 50 through 63 Processing helix chain 'Y' and resid 81 through 92 Processing helix chain 'Y' and resid 103 through 105 No H-bonds generated for 'chain 'Y' and resid 103 through 105' Processing helix chain 'Y' and resid 113 through 124 removed outlier: 4.047A pdb=" N SER Y 124 " --> pdb=" O ALA Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 173 through 180 Processing helix chain 'Y' and resid 206 through 208 No H-bonds generated for 'chain 'Y' and resid 206 through 208' Processing helix chain 'Y' and resid 241 through 249 removed outlier: 3.612A pdb=" N SER Y 249 " --> pdb=" O ASP Y 245 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 267 through 283 Processing helix chain 'Y' and resid 303 through 311 Processing helix chain 'Y' and resid 340 through 342 No H-bonds generated for 'chain 'Y' and resid 340 through 342' Processing helix chain 'Y' and resid 345 through 349 Processing helix chain 'Y' and resid 361 through 374 Processing helix chain 'Y' and resid 381 through 393 Processing helix chain 'Y' and resid 396 through 412 removed outlier: 3.822A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) Processing helix chain 'Y' and resid 420 through 429 Processing helix chain 'Y' and resid 433 through 446 removed outlier: 3.621A pdb=" N ASN Y 443 " --> pdb=" O TYR Y 439 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER Y 445 " --> pdb=" O GLN Y 441 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLN Y 446 " --> pdb=" O GLU Y 442 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'Q' and resid 949 through 954 removed outlier: 6.054A pdb=" N VAL Q1419 " --> pdb=" O ILE Q 950 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL Q 952 " --> pdb=" O VAL Q1419 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ARG Q1421 " --> pdb=" O VAL Q 952 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N CYS Q 954 " --> pdb=" O ARG Q1421 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU Q1423 " --> pdb=" O CYS Q 954 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU Q1422 " --> pdb=" O PHE Q1391 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'Q' and resid 1026 through 1028 Processing sheet with id= C, first strand: chain 'Q' and resid 1082 through 1084 removed outlier: 6.950A pdb=" N THR Q1220 " --> pdb=" O TYR Q1083 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'R' and resid 40 through 44 Processing sheet with id= E, first strand: chain 'R' and resid 67 through 72 removed outlier: 3.749A pdb=" N LYS R 77 " --> pdb=" O ASP R 72 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'R' and resid 700 through 702 removed outlier: 6.824A pdb=" N VAL R 668 " --> pdb=" O ASN R 701 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU R 185 " --> pdb=" O LEU R 669 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR R 671 " --> pdb=" O LEU R 185 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE R 187 " --> pdb=" O THR R 671 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 275 through 278 Processing sheet with id= H, first strand: chain 'T' and resid 368 through 372 removed outlier: 3.558A pdb=" N LEU T 368 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL T 336 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU T 77 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU T 338 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N GLY T 79 " --> pdb=" O LEU T 338 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER T 340 " --> pdb=" O GLY T 79 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'T' and resid 301 through 305 Processing sheet with id= J, first strand: chain 'T' and resid 175 through 181 removed outlier: 4.213A pdb=" N HIS T 165 " --> pdb=" O GLU T 150 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU T 150 " --> pdb=" O HIS T 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE T 167 " --> pdb=" O THR T 148 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU T 146 " --> pdb=" O GLY T 169 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS T 171 " --> pdb=" O VAL T 144 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL T 144 " --> pdb=" O LYS T 171 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP T 198 " --> pdb=" O VAL T 144 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR T 201 " --> pdb=" O ARG T 211 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ARG T 211 " --> pdb=" O TYR T 201 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLU T 203 " --> pdb=" O VAL T 209 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL T 209 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'T' and resid 344 through 346 Processing sheet with id= L, first strand: chain 'U' and resid 351 through 355 removed outlier: 7.112A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL U 321 " --> pdb=" O VAL U 71 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL U 73 " --> pdb=" O VAL U 321 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N MET U 323 " --> pdb=" O VAL U 73 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'U' and resid 287 through 290 Processing sheet with id= N, first strand: chain 'U' and resid 166 through 171 removed outlier: 4.109A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS U 161 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL U 140 " --> pdb=" O LYS U 161 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP U 188 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY U 203 " --> pdb=" O VAL U 189 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER U 191 " --> pdb=" O LYS U 201 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LYS U 201 " --> pdb=" O SER U 191 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'V' and resid 368 through 371 removed outlier: 6.544A pdb=" N VAL V 336 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU V 77 " --> pdb=" O VAL V 336 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU V 338 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'V' and resid 301 through 305 removed outlier: 3.506A pdb=" N ILE V 304 " --> pdb=" O GLY V 130 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V' and resid 175 through 181 removed outlier: 3.737A pdb=" N GLY V 175 " --> pdb=" O SER V 172 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU V 146 " --> pdb=" O GLY V 169 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS V 171 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL V 144 " --> pdb=" O LYS V 171 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP V 198 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY V 213 " --> pdb=" O VAL V 199 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR V 201 " --> pdb=" O ARG V 211 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ARG V 211 " --> pdb=" O TYR V 201 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLU V 203 " --> pdb=" O VAL V 209 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL V 209 " --> pdb=" O GLU V 203 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'V' and resid 344 through 346 Processing sheet with id= S, first strand: chain 'W' and resid 351 through 355 removed outlier: 6.865A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL W 321 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL W 73 " --> pdb=" O VAL W 321 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET W 323 " --> pdb=" O VAL W 73 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'W' and resid 286 through 290 Processing sheet with id= U, first strand: chain 'W' and resid 166 through 171 removed outlier: 4.100A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU W 142 " --> pdb=" O THR W 159 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE W 190 " --> pdb=" O GLY W 138 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP W 188 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER W 191 " --> pdb=" O LYS W 201 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS W 201 " --> pdb=" O SER W 191 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ASP W 193 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE W 199 " --> pdb=" O ASP W 193 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'X' and resid 367 through 371 removed outlier: 7.193A pdb=" N ALA X 74 " --> pdb=" O LEU X 368 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL X 336 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU X 77 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU X 338 " --> pdb=" O LEU X 77 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 301 through 305 removed outlier: 3.661A pdb=" N VAL X 139 " --> pdb=" O LYS X 239 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS X 239 " --> pdb=" O VAL X 139 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 175 through 181 removed outlier: 3.509A pdb=" N GLY X 175 " --> pdb=" O SER X 172 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL X 166 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS X 165 " --> pdb=" O GLU X 150 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU X 146 " --> pdb=" O GLY X 169 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS X 171 " --> pdb=" O VAL X 144 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL X 144 " --> pdb=" O LYS X 171 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP X 198 " --> pdb=" O VAL X 144 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY X 213 " --> pdb=" O VAL X 199 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR X 201 " --> pdb=" O ARG X 211 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG X 211 " --> pdb=" O TYR X 201 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'X' and resid 344 through 346 Processing sheet with id= Z, first strand: chain 'Y' and resid 352 through 355 removed outlier: 3.700A pdb=" N ILE Y 352 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Y' and resid 230 through 240 removed outlier: 3.527A pdb=" N LYS Y 233 " --> pdb=" O THR Y 133 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU Y 287 " --> pdb=" O LYS Y 128 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Y' and resid 166 through 171 removed outlier: 4.215A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU Y 142 " --> pdb=" O THR Y 159 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS Y 161 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL Y 140 " --> pdb=" O LYS Y 161 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP Y 188 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY Y 203 " --> pdb=" O VAL Y 189 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N SER Y 191 " --> pdb=" O LYS Y 201 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LYS Y 201 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ASP Y 193 " --> pdb=" O ILE Y 199 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE Y 199 " --> pdb=" O ASP Y 193 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Y' and resid 329 through 331 Processing sheet with id= AD, first strand: chain 'Z' and resid 307 through 310 removed outlier: 3.511A pdb=" N ARG Z 307 " --> pdb=" O CYS Z 318 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 3066 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.56 Time building geometry restraints manager: 11.45 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: 9550 1.34 - 1.46: 5814 1.46 - 1.58: 13554 1.58 - 1.71: 18 1.71 - 1.83: 166 Bond restraints: 29102 Sorted by residual: bond pdb=" N TYR X 229 " pdb=" CA TYR X 229 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 6.11e+00 bond pdb=" N PHE X 222 " pdb=" CA PHE X 222 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.31e-02 5.83e+03 5.67e+00 bond pdb=" N LEU X 224 " pdb=" CA LEU X 224 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.56e+00 bond pdb=" N GLU X 227 " pdb=" CA GLU X 227 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.26e-02 6.30e+03 5.47e+00 bond pdb=" N GLU X 225 " pdb=" CA GLU X 225 " ideal model delta sigma weight residual 1.461 1.489 -0.028 1.20e-02 6.94e+03 5.30e+00 ... (remaining 29097 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.70: 557 105.70 - 113.30: 16409 113.30 - 120.89: 13286 120.89 - 128.48: 9005 128.48 - 136.08: 116 Bond angle restraints: 39373 Sorted by residual: angle pdb=" CB MET W 175 " pdb=" CG MET W 175 " pdb=" SD MET W 175 " ideal model delta sigma weight residual 112.70 130.82 -18.12 3.00e+00 1.11e-01 3.65e+01 angle pdb=" CB MET Q1291 " pdb=" CG MET Q1291 " pdb=" SD MET Q1291 " ideal model delta sigma weight residual 112.70 130.16 -17.46 3.00e+00 1.11e-01 3.39e+01 angle pdb=" CB MET Q1405 " pdb=" CG MET Q1405 " pdb=" SD MET Q1405 " ideal model delta sigma weight residual 112.70 129.37 -16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" CA LEU Q 963 " pdb=" CB LEU Q 963 " pdb=" CG LEU Q 963 " ideal model delta sigma weight residual 116.30 134.86 -18.56 3.50e+00 8.16e-02 2.81e+01 angle pdb=" CA MET Q1405 " pdb=" CB MET Q1405 " pdb=" CG MET Q1405 " ideal model delta sigma weight residual 114.10 124.26 -10.16 2.00e+00 2.50e-01 2.58e+01 ... (remaining 39368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.74: 17104 33.74 - 67.49: 721 67.49 - 101.23: 48 101.23 - 134.98: 5 134.98 - 168.72: 2 Dihedral angle restraints: 17880 sinusoidal: 7318 harmonic: 10562 Sorted by residual: dihedral pdb=" C5' ADP U 501 " pdb=" O5' ADP U 501 " pdb=" PA ADP U 501 " pdb=" O2A ADP U 501 " ideal model delta sinusoidal sigma weight residual 300.00 131.28 168.72 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O1B ADP U 501 " pdb=" O3A ADP U 501 " pdb=" PB ADP U 501 " pdb=" PA ADP U 501 " ideal model delta sinusoidal sigma weight residual 300.00 162.10 137.90 1 2.00e+01 2.50e-03 4.18e+01 dihedral pdb=" O1B ADP V 501 " pdb=" O3A ADP V 501 " pdb=" PB ADP V 501 " pdb=" PA ADP V 501 " ideal model delta sinusoidal sigma weight residual 300.00 172.69 127.30 1 2.00e+01 2.50e-03 3.85e+01 ... (remaining 17877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4003 0.072 - 0.144: 565 0.144 - 0.216: 48 0.216 - 0.288: 3 0.288 - 0.360: 1 Chirality restraints: 4620 Sorted by residual: chirality pdb=" CB ILE Q 971 " pdb=" CA ILE Q 971 " pdb=" CG1 ILE Q 971 " pdb=" CG2 ILE Q 971 " both_signs ideal model delta sigma weight residual False 2.64 3.00 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB VAL Q1152 " pdb=" CA VAL Q1152 " pdb=" CG1 VAL Q1152 " pdb=" CG2 VAL Q1152 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ASP X 352 " pdb=" N ASP X 352 " pdb=" C ASP X 352 " pdb=" CB ASP X 352 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 4617 not shown) Planarity restraints: 5040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN Q1397 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO Q1398 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO Q1398 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO Q1398 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP Y 95 " 0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ASP Y 95 " -0.064 2.00e-02 2.50e+03 pdb=" O ASP Y 95 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL Y 96 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU T 119 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.64e+00 pdb=" CD GLU T 119 " 0.054 2.00e-02 2.50e+03 pdb=" OE1 GLU T 119 " -0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU T 119 " -0.018 2.00e-02 2.50e+03 ... (remaining 5037 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 190 2.54 - 3.13: 20114 3.13 - 3.72: 43760 3.72 - 4.31: 60066 4.31 - 4.90: 101487 Nonbonded interactions: 225617 Sorted by model distance: nonbonded pdb=" NE2 HIS U 153 " pdb=" OE1 GLN U 155 " model vdw 1.956 2.520 nonbonded pdb=" OG SER Y 24 " pdb=" OE2 GLU Y 374 " model vdw 2.271 2.440 nonbonded pdb=" OG1 THR T 248 " pdb=" OD1 ASP T 251 " model vdw 2.273 2.440 nonbonded pdb=" O PRO Y 76 " pdb=" OG1 THR Y 79 " model vdw 2.282 2.440 nonbonded pdb=" O LEU Y 255 " pdb=" OG1 THR Y 259 " model vdw 2.285 2.440 ... (remaining 225612 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 'T' and (resid 22 through 463 or resid 501)) selection = (chain 'V' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 463 or resid 501)) selection = (chain 'X' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 463 or resid 501)) } ncs_group { reference = (chain 'U' and (resid 18 through 459 or resid 501)) selection = (chain 'W' and (resid 18 through 210 or resid 221 through 459 or resid 501)) selection = (chain 'Y' and (resid 18 through 210 or resid 221 through 459 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 22.960 Check model and map are aligned: 0.430 Set scattering table: 0.240 Process input model: 72.460 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.130 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 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 0.066 29102 Z= 0.268 Angle : 0.828 18.562 39373 Z= 0.429 Chirality : 0.050 0.360 4620 Planarity : 0.005 0.103 5040 Dihedral : 17.559 168.724 11060 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.03 % Allowed : 25.21 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.12), residues: 3618 helix: -1.49 (0.11), residues: 1493 sheet: 0.73 (0.21), residues: 636 loop : -1.45 (0.14), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q1361 HIS 0.023 0.001 HIS Q1342 PHE 0.025 0.001 PHE Z 293 TYR 0.016 0.002 TYR V 462 ARG 0.006 0.001 ARG V 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1045 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1012 ASN cc_start: 0.7654 (t0) cc_final: 0.7433 (t0) REVERT: Q 1016 LEU cc_start: 0.7228 (mt) cc_final: 0.6991 (mt) REVERT: Q 1112 LYS cc_start: 0.8375 (mtpp) cc_final: 0.8076 (mtpp) REVERT: Q 1150 LYS cc_start: 0.7561 (tppt) cc_final: 0.7331 (mmmm) REVERT: Q 1189 SER cc_start: 0.8108 (t) cc_final: 0.7438 (p) REVERT: Q 1228 HIS cc_start: 0.7337 (t-90) cc_final: 0.6766 (t70) REVERT: Q 1244 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7794 (mm-40) REVERT: Q 1255 TYR cc_start: 0.7779 (t80) cc_final: 0.6837 (t80) REVERT: Q 1270 LYS cc_start: 0.7629 (ptmm) cc_final: 0.7222 (ptpp) REVERT: Q 1284 SER cc_start: 0.8021 (p) cc_final: 0.7665 (t) REVERT: Q 1287 SER cc_start: 0.7866 (m) cc_final: 0.7396 (t) REVERT: Q 1300 LYS cc_start: 0.8337 (mttt) cc_final: 0.8135 (mttt) REVERT: Q 1316 HIS cc_start: 0.7760 (m-70) cc_final: 0.7385 (m-70) REVERT: Q 1327 MET cc_start: 0.6067 (mmm) cc_final: 0.5701 (mmm) REVERT: Q 1432 MET cc_start: 0.4327 (tpp) cc_final: 0.4075 (tpp) REVERT: R 19 PRO cc_start: 0.8045 (Cg_exo) cc_final: 0.7660 (Cg_endo) REVERT: R 62 ILE cc_start: 0.7619 (mt) cc_final: 0.7397 (mm) REVERT: R 63 PHE cc_start: 0.7586 (p90) cc_final: 0.7326 (p90) REVERT: R 82 VAL cc_start: 0.7716 (t) cc_final: 0.7370 (t) REVERT: R 85 ASP cc_start: 0.8787 (m-30) cc_final: 0.8555 (m-30) REVERT: R 93 ARG cc_start: 0.8545 (tmm-80) cc_final: 0.8080 (ttp-170) REVERT: R 95 GLN cc_start: 0.8923 (mt0) cc_final: 0.8604 (mt0) REVERT: R 97 ARG cc_start: 0.7842 (ttp-110) cc_final: 0.7540 (ttp-110) REVERT: R 113 GLU cc_start: 0.7666 (tt0) cc_final: 0.7339 (tt0) REVERT: R 145 SER cc_start: 0.6876 (p) cc_final: 0.6543 (t) REVERT: R 146 GLN cc_start: 0.7515 (tt0) cc_final: 0.7218 (tt0) REVERT: R 147 ARG cc_start: 0.7904 (ptp90) cc_final: 0.7595 (ptm160) REVERT: R 164 THR cc_start: 0.6558 (p) cc_final: 0.5465 (m) REVERT: R 182 LYS cc_start: 0.7697 (mmtp) cc_final: 0.7490 (mmmm) REVERT: R 193 ASP cc_start: 0.7438 (p0) cc_final: 0.7205 (p0) REVERT: R 201 ASP cc_start: 0.7728 (m-30) cc_final: 0.7486 (m-30) REVERT: R 240 TYR cc_start: 0.7827 (t80) cc_final: 0.7321 (t80) REVERT: R 242 GLN cc_start: 0.7917 (mt0) cc_final: 0.7503 (mt0) REVERT: R 244 GLU cc_start: 0.7631 (tt0) cc_final: 0.7140 (tt0) REVERT: R 249 ASP cc_start: 0.8010 (m-30) cc_final: 0.7684 (m-30) REVERT: R 256 ASN cc_start: 0.7195 (t0) cc_final: 0.6982 (t0) REVERT: R 258 ASP cc_start: 0.7999 (m-30) cc_final: 0.7780 (m-30) REVERT: R 260 ASP cc_start: 0.7566 (m-30) cc_final: 0.7165 (m-30) REVERT: R 262 GLU cc_start: 0.7775 (mp0) cc_final: 0.7009 (mp0) REVERT: R 264 ILE cc_start: 0.8279 (tt) cc_final: 0.7904 (tp) REVERT: R 269 ASN cc_start: 0.7069 (t0) cc_final: 0.6425 (t0) REVERT: R 273 ASN cc_start: 0.8064 (m110) cc_final: 0.7081 (t0) REVERT: R 277 VAL cc_start: 0.7734 (m) cc_final: 0.7349 (p) REVERT: R 596 ARG cc_start: 0.8151 (mpt180) cc_final: 0.7838 (mmt-90) REVERT: R 616 VAL cc_start: 0.8073 (t) cc_final: 0.7849 (p) REVERT: R 653 GLN cc_start: 0.6791 (tp40) cc_final: 0.6572 (tm-30) REVERT: R 656 LYS cc_start: 0.7130 (tttt) cc_final: 0.6908 (tttt) REVERT: R 677 VAL cc_start: 0.8632 (t) cc_final: 0.8344 (m) REVERT: R 709 ASP cc_start: 0.7179 (m-30) cc_final: 0.6926 (m-30) REVERT: R 724 TYR cc_start: 0.7841 (t80) cc_final: 0.7562 (t80) REVERT: R 726 LYS cc_start: 0.8202 (mptt) cc_final: 0.8000 (mtmm) REVERT: R 729 ILE cc_start: 0.6827 (mm) cc_final: 0.6419 (tp) REVERT: R 735 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7948 (mp0) REVERT: R 736 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7180 (tm-30) REVERT: R 746 LYS cc_start: 0.8768 (mttt) cc_final: 0.8564 (mtpp) REVERT: S 114 LYS cc_start: 0.7893 (mttp) cc_final: 0.7638 (mttp) REVERT: S 121 LEU cc_start: 0.7288 (mt) cc_final: 0.6892 (mt) REVERT: S 157 LYS cc_start: 0.7884 (ttmm) cc_final: 0.7671 (ttmm) REVERT: T 23 ARG cc_start: 0.7650 (mmm160) cc_final: 0.7202 (mtp180) REVERT: T 31 LYS cc_start: 0.8194 (mmtp) cc_final: 0.7978 (mmtm) REVERT: T 99 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7941 (ttpp) REVERT: T 122 MET cc_start: 0.7446 (tpt) cc_final: 0.7149 (mmm) REVERT: T 134 LYS cc_start: 0.8336 (mtpp) cc_final: 0.8101 (mtmm) REVERT: T 180 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.8076 (mtp85) REVERT: T 195 SER cc_start: 0.8064 (m) cc_final: 0.7772 (t) REVERT: T 232 LEU cc_start: 0.8389 (mt) cc_final: 0.8178 (mt) REVERT: T 276 LYS cc_start: 0.7938 (pttt) cc_final: 0.7730 (pttt) REVERT: T 295 TYR cc_start: 0.7769 (m-80) cc_final: 0.7521 (m-80) REVERT: T 302 GLU cc_start: 0.7789 (tt0) cc_final: 0.7506 (tt0) REVERT: T 312 GLU cc_start: 0.7580 (mp0) cc_final: 0.6747 (mp0) REVERT: T 317 ASP cc_start: 0.7727 (t0) cc_final: 0.7141 (t0) REVERT: T 345 THR cc_start: 0.8061 (m) cc_final: 0.7564 (p) REVERT: T 347 VAL cc_start: 0.7954 (t) cc_final: 0.7628 (p) REVERT: T 385 GLU cc_start: 0.7621 (tt0) cc_final: 0.7241 (tm-30) REVERT: T 389 THR cc_start: 0.7040 (m) cc_final: 0.6475 (m) REVERT: T 441 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7274 (tp30) REVERT: U 32 ASP cc_start: 0.7503 (m-30) cc_final: 0.7154 (m-30) REVERT: U 65 THR cc_start: 0.7312 (p) cc_final: 0.7097 (t) REVERT: U 105 GLU cc_start: 0.7971 (tt0) cc_final: 0.7620 (tt0) REVERT: U 107 PHE cc_start: 0.8469 (m-80) cc_final: 0.7887 (m-80) REVERT: U 115 GLU cc_start: 0.7474 (tp30) cc_final: 0.7268 (tp30) REVERT: U 139 GLU cc_start: 0.8079 (tt0) cc_final: 0.7808 (tt0) REVERT: U 142 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6481 (tm-30) REVERT: U 157 LYS cc_start: 0.7655 (mttt) cc_final: 0.7136 (mttm) REVERT: U 176 ILE cc_start: 0.7747 (mt) cc_final: 0.7368 (tt) REVERT: U 193 ASP cc_start: 0.7370 (t0) cc_final: 0.6749 (t0) REVERT: U 198 LYS cc_start: 0.7966 (ttpt) cc_final: 0.7748 (tttm) REVERT: U 199 ILE cc_start: 0.7038 (mt) cc_final: 0.6535 (tt) REVERT: U 228 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6682 (mm-30) REVERT: U 233 LYS cc_start: 0.7343 (mmmt) cc_final: 0.6851 (mmmt) REVERT: U 264 GLU cc_start: 0.7984 (mt-10) cc_final: 0.6836 (mt-10) REVERT: U 282 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7063 (mt-10) REVERT: U 283 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6661 (mt-10) REVERT: U 311 ARG cc_start: 0.7852 (mmt180) cc_final: 0.7648 (mmt180) REVERT: U 322 MET cc_start: 0.7473 (mtt) cc_final: 0.7245 (mtp) REVERT: U 339 SER cc_start: 0.8293 (m) cc_final: 0.8075 (t) REVERT: U 359 TYR cc_start: 0.8176 (m-80) cc_final: 0.7907 (m-80) REVERT: U 374 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7436 (mm-30) REVERT: U 376 GLU cc_start: 0.7376 (pm20) cc_final: 0.7156 (pm20) REVERT: U 379 LEU cc_start: 0.8373 (mt) cc_final: 0.8142 (mt) REVERT: U 385 ASP cc_start: 0.7577 (m-30) cc_final: 0.7374 (m-30) REVERT: U 413 ARG cc_start: 0.7521 (mtm110) cc_final: 0.7229 (ptm-80) REVERT: U 422 ASP cc_start: 0.7995 (m-30) cc_final: 0.7741 (m-30) REVERT: U 432 ASP cc_start: 0.7934 (p0) cc_final: 0.7705 (p0) REVERT: U 438 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7360 (tppt) REVERT: U 439 TYR cc_start: 0.7210 (m-80) cc_final: 0.6812 (m-10) REVERT: U 451 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7149 (mp10) REVERT: V 36 ASP cc_start: 0.6983 (m-30) cc_final: 0.6523 (m-30) REVERT: V 40 VAL cc_start: 0.7212 (t) cc_final: 0.6492 (t) REVERT: V 42 LYS cc_start: 0.7262 (mtmm) cc_final: 0.6429 (tttt) REVERT: V 63 ASP cc_start: 0.7841 (t0) cc_final: 0.7634 (t0) REVERT: V 69 LYS cc_start: 0.7821 (mttm) cc_final: 0.7323 (mtmm) REVERT: V 99 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7619 (mtpt) REVERT: V 177 LYS cc_start: 0.8073 (ttmt) cc_final: 0.7619 (ttpp) REVERT: V 178 THR cc_start: 0.8234 (m) cc_final: 0.7912 (p) REVERT: V 187 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6733 (mm-30) REVERT: V 193 LYS cc_start: 0.7548 (mtpt) cc_final: 0.7295 (mtpt) REVERT: V 203 GLU cc_start: 0.7895 (pt0) cc_final: 0.7463 (mt-10) REVERT: V 214 ARG cc_start: 0.7236 (mmt180) cc_final: 0.6656 (mmm-85) REVERT: V 227 GLU cc_start: 0.7452 (tt0) cc_final: 0.7219 (mm-30) REVERT: V 264 ASP cc_start: 0.6536 (p0) cc_final: 0.6318 (p0) REVERT: V 287 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7538 (mm-30) REVERT: V 294 LYS cc_start: 0.7535 (tppt) cc_final: 0.7330 (tppt) REVERT: V 297 ASP cc_start: 0.7783 (t0) cc_final: 0.7414 (t0) REVERT: V 302 GLU cc_start: 0.7472 (pt0) cc_final: 0.7164 (pt0) REVERT: V 315 MET cc_start: 0.7927 (mmp) cc_final: 0.7726 (mmm) REVERT: V 326 LYS cc_start: 0.7632 (tmmt) cc_final: 0.7166 (tppt) REVERT: V 355 SER cc_start: 0.8631 (m) cc_final: 0.7931 (p) REVERT: V 385 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7126 (mm-30) REVERT: V 392 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7694 (mtt-85) REVERT: W 38 ARG cc_start: 0.7958 (mtm-85) cc_final: 0.7575 (mtt90) REVERT: W 58 LEU cc_start: 0.7254 (tp) cc_final: 0.7022 (tt) REVERT: W 134 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6641 (mm-30) REVERT: W 142 GLU cc_start: 0.8227 (tt0) cc_final: 0.8022 (tt0) REVERT: W 146 ASP cc_start: 0.8422 (m-30) cc_final: 0.7744 (m-30) REVERT: W 154 LYS cc_start: 0.8277 (mtpp) cc_final: 0.8049 (mtmt) REVERT: W 160 ILE cc_start: 0.8255 (tt) cc_final: 0.7807 (tp) REVERT: W 181 LYS cc_start: 0.8011 (ttpp) cc_final: 0.7727 (ttpp) REVERT: W 189 VAL cc_start: 0.7456 (t) cc_final: 0.7163 (m) REVERT: W 266 ARG cc_start: 0.7151 (mtm-85) cc_final: 0.6615 (mtm-85) REVERT: W 285 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7905 (ttmm) REVERT: W 297 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7560 (mm-30) REVERT: W 302 ASP cc_start: 0.7247 (t0) cc_final: 0.6573 (t0) REVERT: W 304 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6775 (mp0) REVERT: W 311 ARG cc_start: 0.7626 (mmt180) cc_final: 0.7373 (mmp-170) REVERT: W 322 MET cc_start: 0.8074 (ttm) cc_final: 0.7811 (ttm) REVERT: W 330 SER cc_start: 0.8148 (p) cc_final: 0.7906 (p) REVERT: W 333 ARG cc_start: 0.8066 (mtm180) cc_final: 0.7787 (mtm180) REVERT: W 338 LYS cc_start: 0.8271 (mtpt) cc_final: 0.7921 (mtmt) REVERT: W 357 LYS cc_start: 0.7779 (pptt) cc_final: 0.7278 (pptt) REVERT: W 374 GLU cc_start: 0.7371 (tp30) cc_final: 0.7074 (tp30) REVERT: W 376 GLU cc_start: 0.7244 (mp0) cc_final: 0.6909 (mp0) REVERT: W 378 GLU cc_start: 0.7708 (mp0) cc_final: 0.7006 (tm-30) REVERT: W 381 SER cc_start: 0.7618 (m) cc_final: 0.7195 (p) REVERT: W 385 ASP cc_start: 0.7869 (m-30) cc_final: 0.7592 (m-30) REVERT: W 388 THR cc_start: 0.8309 (m) cc_final: 0.8011 (p) REVERT: W 393 GLU cc_start: 0.7857 (tt0) cc_final: 0.7359 (mt-10) REVERT: W 413 ARG cc_start: 0.7702 (mtp180) cc_final: 0.7368 (mtm180) REVERT: W 442 GLU cc_start: 0.6917 (pt0) cc_final: 0.6643 (pp20) REVERT: W 443 ASN cc_start: 0.6549 (m110) cc_final: 0.5663 (m110) REVERT: W 449 ASP cc_start: 0.7343 (t70) cc_final: 0.6915 (t70) REVERT: W 451 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7575 (mm110) REVERT: X 100 VAL cc_start: 0.8098 (t) cc_final: 0.7843 (m) REVERT: X 114 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7566 (mt-10) REVERT: X 141 GLU cc_start: 0.7448 (pm20) cc_final: 0.7035 (pm20) REVERT: X 144 VAL cc_start: 0.8475 (t) cc_final: 0.8144 (p) REVERT: X 172 SER cc_start: 0.8030 (m) cc_final: 0.7743 (t) REVERT: X 177 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7748 (ttmm) REVERT: X 178 THR cc_start: 0.8006 (p) cc_final: 0.7439 (t) REVERT: X 179 LEU cc_start: 0.7742 (mt) cc_final: 0.7449 (mp) REVERT: X 182 ASP cc_start: 0.7659 (t70) cc_final: 0.7459 (m-30) REVERT: X 187 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7484 (mm-30) REVERT: X 196 ILE cc_start: 0.7796 (mt) cc_final: 0.7435 (mm) REVERT: X 198 ASP cc_start: 0.7344 (m-30) cc_final: 0.6698 (m-30) REVERT: X 210 LYS cc_start: 0.7070 (ptmt) cc_final: 0.6831 (ptmt) REVERT: X 221 GLU cc_start: 0.7479 (tp30) cc_final: 0.7096 (tp30) REVERT: X 226 THR cc_start: 0.7280 (OUTLIER) cc_final: 0.7017 (p) REVERT: X 239 LYS cc_start: 0.7904 (pttt) cc_final: 0.7613 (pttm) REVERT: X 240 LYS cc_start: 0.8217 (mtmt) cc_final: 0.8007 (mtmt) REVERT: X 251 ASP cc_start: 0.6906 (m-30) cc_final: 0.6637 (m-30) REVERT: X 282 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6486 (tm-30) REVERT: X 295 TYR cc_start: 0.7781 (m-80) cc_final: 0.7186 (m-80) REVERT: X 315 MET cc_start: 0.7468 (mmp) cc_final: 0.7177 (mmm) REVERT: X 325 ASN cc_start: 0.8304 (m-40) cc_final: 0.7895 (m-40) REVERT: X 341 ASN cc_start: 0.8452 (p0) cc_final: 0.8231 (p0) REVERT: X 345 THR cc_start: 0.8084 (p) cc_final: 0.7754 (p) REVERT: X 348 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7083 (mtm180) REVERT: X 409 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7481 (tm-30) REVERT: X 432 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7624 (mmmm) REVERT: X 434 ILE cc_start: 0.7443 (mt) cc_final: 0.7159 (tt) REVERT: X 438 ASP cc_start: 0.7825 (m-30) cc_final: 0.7570 (m-30) REVERT: Y 34 ASN cc_start: 0.7774 (t0) cc_final: 0.7491 (t0) REVERT: Y 59 LYS cc_start: 0.7871 (ttmm) cc_final: 0.7654 (mmmt) REVERT: Y 107 PHE cc_start: 0.8191 (m-80) cc_final: 0.7826 (m-80) REVERT: Y 115 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6186 (tm-30) REVERT: Y 144 GLN cc_start: 0.6659 (tt0) cc_final: 0.6250 (tt0) REVERT: Y 188 ASP cc_start: 0.7996 (t0) cc_final: 0.7775 (m-30) REVERT: Y 206 PHE cc_start: 0.7800 (m-80) cc_final: 0.7558 (m-80) REVERT: Y 210 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7444 (mmm160) REVERT: Y 264 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7648 (mt-10) REVERT: Y 281 LYS cc_start: 0.7322 (tttm) cc_final: 0.7053 (ttpp) REVERT: Y 316 GLU cc_start: 0.7274 (mt-10) cc_final: 0.7004 (mt-10) REVERT: Y 317 PHE cc_start: 0.8504 (m-80) cc_final: 0.8120 (m-80) REVERT: Y 322 MET cc_start: 0.8264 (mtp) cc_final: 0.8047 (mtm) REVERT: Y 349 ASP cc_start: 0.7848 (t0) cc_final: 0.7630 (t70) REVERT: Y 357 LYS cc_start: 0.7746 (mttm) cc_final: 0.7394 (mmtp) REVERT: Y 361 GLU cc_start: 0.7293 (tt0) cc_final: 0.7057 (tp30) REVERT: Y 373 GLN cc_start: 0.7773 (tt0) cc_final: 0.7572 (tt0) REVERT: Y 374 GLU cc_start: 0.7229 (tt0) cc_final: 0.6486 (tt0) REVERT: Y 378 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6721 (mm-30) REVERT: Y 392 VAL cc_start: 0.7837 (t) cc_final: 0.7433 (p) REVERT: Y 401 ASN cc_start: 0.7937 (m-40) cc_final: 0.7736 (m-40) REVERT: Y 443 ASN cc_start: 0.7712 (m110) cc_final: 0.7359 (m110) REVERT: Y 444 GLU cc_start: 0.7923 (tt0) cc_final: 0.7325 (tp30) REVERT: Y 453 ASN cc_start: 0.8233 (m110) cc_final: 0.7809 (m-40) REVERT: Z 307 ARG cc_start: 0.8097 (ttm-80) cc_final: 0.7861 (tpp80) REVERT: Z 311 ARG cc_start: 0.7966 (ttm110) cc_final: 0.7510 (mtp85) REVERT: Z 312 TYR cc_start: 0.8017 (m-80) cc_final: 0.7740 (m-80) outliers start: 1 outliers final: 0 residues processed: 1045 average time/residue: 0.4629 time to fit residues: 723.1220 Evaluate side-chains 905 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 904 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 226 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 0.2980 chunk 273 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 93 optimal weight: 0.0370 chunk 184 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 282 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1213 ASN Q1342 HIS R 121 HIS R 132 ASN R 175 ASN ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 ASN T 190 GLN ** T 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 440 ASN U 230 GLN V 29 HIS V 154 ASN ** V 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN X 190 GLN X 271 GLN X 331 ASN Y 415 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29102 Z= 0.216 Angle : 0.562 9.221 39373 Z= 0.279 Chirality : 0.043 0.198 4620 Planarity : 0.004 0.065 5040 Dihedral : 7.053 151.286 4005 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.75 % Allowed : 24.30 % Favored : 72.95 % 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: -0.61 (0.13), residues: 3618 helix: -0.07 (0.13), residues: 1482 sheet: 0.70 (0.20), residues: 652 loop : -1.17 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q1361 HIS 0.008 0.001 HIS Q1342 PHE 0.021 0.001 PHE R 70 TYR 0.019 0.001 TYR R 231 ARG 0.007 0.000 ARG X 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 943 time to evaluate : 3.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1112 LYS cc_start: 0.8351 (mtpp) cc_final: 0.8006 (mtpp) REVERT: Q 1134 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7653 (mt-10) REVERT: Q 1146 THR cc_start: 0.7073 (p) cc_final: 0.6352 (m) REVERT: Q 1150 LYS cc_start: 0.7588 (tppt) cc_final: 0.7282 (tppt) REVERT: Q 1151 ARG cc_start: 0.7697 (ttp80) cc_final: 0.7403 (mtm110) REVERT: Q 1189 SER cc_start: 0.8011 (t) cc_final: 0.7429 (p) REVERT: Q 1208 ARG cc_start: 0.7820 (ttm170) cc_final: 0.7590 (ptm160) REVERT: Q 1255 TYR cc_start: 0.7766 (t80) cc_final: 0.7031 (t80) REVERT: Q 1287 SER cc_start: 0.7947 (m) cc_final: 0.7498 (t) REVERT: Q 1300 LYS cc_start: 0.8363 (mttt) cc_final: 0.8160 (mttt) REVERT: Q 1316 HIS cc_start: 0.7744 (m-70) cc_final: 0.7220 (m-70) REVERT: Q 1327 MET cc_start: 0.6057 (mmm) cc_final: 0.5630 (mmm) REVERT: R 19 PRO cc_start: 0.8033 (Cg_exo) cc_final: 0.7528 (Cg_endo) REVERT: R 79 PHE cc_start: 0.7938 (m-10) cc_final: 0.7694 (m-80) REVERT: R 85 ASP cc_start: 0.8844 (m-30) cc_final: 0.8631 (m-30) REVERT: R 93 ARG cc_start: 0.8543 (tmm-80) cc_final: 0.8022 (ttp-170) REVERT: R 95 GLN cc_start: 0.8929 (mt0) cc_final: 0.8628 (mt0) REVERT: R 97 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7606 (ttp-110) REVERT: R 145 SER cc_start: 0.6900 (p) cc_final: 0.6664 (t) REVERT: R 146 GLN cc_start: 0.7611 (tt0) cc_final: 0.7264 (tt0) REVERT: R 193 ASP cc_start: 0.7477 (p0) cc_final: 0.7255 (p0) REVERT: R 240 TYR cc_start: 0.7858 (t80) cc_final: 0.7610 (t80) REVERT: R 242 GLN cc_start: 0.7843 (mt0) cc_final: 0.7339 (mt0) REVERT: R 244 GLU cc_start: 0.7703 (tt0) cc_final: 0.7235 (tt0) REVERT: R 258 ASP cc_start: 0.8123 (m-30) cc_final: 0.7869 (m-30) REVERT: R 260 ASP cc_start: 0.7571 (m-30) cc_final: 0.7135 (m-30) REVERT: R 262 GLU cc_start: 0.7755 (mp0) cc_final: 0.7057 (mp0) REVERT: R 264 ILE cc_start: 0.8283 (tt) cc_final: 0.7888 (tp) REVERT: R 269 ASN cc_start: 0.7135 (t0) cc_final: 0.6517 (t0) REVERT: R 596 ARG cc_start: 0.8214 (mpt180) cc_final: 0.8007 (mmt-90) REVERT: R 616 VAL cc_start: 0.8057 (t) cc_final: 0.7783 (p) REVERT: R 677 VAL cc_start: 0.8647 (t) cc_final: 0.8379 (m) REVERT: R 709 ASP cc_start: 0.7281 (m-30) cc_final: 0.7057 (m-30) REVERT: R 723 GLN cc_start: 0.7599 (mp10) cc_final: 0.7118 (mp10) REVERT: R 724 TYR cc_start: 0.7824 (t80) cc_final: 0.7473 (t80) REVERT: R 726 LYS cc_start: 0.8303 (mptt) cc_final: 0.8081 (mtmm) REVERT: R 734 TYR cc_start: 0.8087 (t80) cc_final: 0.7848 (t80) REVERT: R 736 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7178 (tm-30) REVERT: R 744 GLU cc_start: 0.7797 (tp30) cc_final: 0.7403 (tp30) REVERT: S 65 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7538 (pt0) REVERT: S 114 LYS cc_start: 0.7870 (mttp) cc_final: 0.7573 (mttp) REVERT: S 121 LEU cc_start: 0.7390 (mt) cc_final: 0.7157 (mt) REVERT: T 23 ARG cc_start: 0.7657 (mmm160) cc_final: 0.7208 (mtp180) REVERT: T 99 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7912 (ttpp) REVERT: T 105 LEU cc_start: 0.8145 (tp) cc_final: 0.7741 (tp) REVERT: T 122 MET cc_start: 0.7444 (tpt) cc_final: 0.7191 (mmm) REVERT: T 123 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7047 (mt-10) REVERT: T 134 LYS cc_start: 0.8458 (mtpp) cc_final: 0.8128 (mtmm) REVERT: T 195 SER cc_start: 0.8041 (m) cc_final: 0.7742 (t) REVERT: T 227 GLU cc_start: 0.7584 (tp30) cc_final: 0.7188 (tp30) REVERT: T 276 LYS cc_start: 0.7942 (pttt) cc_final: 0.7717 (pttt) REVERT: T 294 LYS cc_start: 0.7667 (ttmm) cc_final: 0.7405 (ttmt) REVERT: T 295 TYR cc_start: 0.7727 (m-80) cc_final: 0.7417 (m-80) REVERT: T 312 GLU cc_start: 0.7548 (mp0) cc_final: 0.6768 (mp0) REVERT: T 317 ASP cc_start: 0.7625 (t0) cc_final: 0.7257 (t0) REVERT: T 347 VAL cc_start: 0.7930 (t) cc_final: 0.7658 (p) REVERT: T 385 GLU cc_start: 0.7638 (tt0) cc_final: 0.7301 (tm-30) REVERT: T 441 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7339 (tp30) REVERT: U 32 ASP cc_start: 0.7598 (m-30) cc_final: 0.7322 (m-30) REVERT: U 65 THR cc_start: 0.7373 (p) cc_final: 0.7158 (t) REVERT: U 105 GLU cc_start: 0.8007 (tt0) cc_final: 0.7693 (tt0) REVERT: U 107 PHE cc_start: 0.8518 (m-80) cc_final: 0.7990 (m-80) REVERT: U 134 GLU cc_start: 0.7677 (tt0) cc_final: 0.7356 (tt0) REVERT: U 139 GLU cc_start: 0.7966 (tt0) cc_final: 0.7686 (tt0) REVERT: U 142 GLU cc_start: 0.6827 (tm-30) cc_final: 0.5932 (tm-30) REVERT: U 144 GLN cc_start: 0.6695 (OUTLIER) cc_final: 0.5566 (mp10) REVERT: U 157 LYS cc_start: 0.7614 (mttt) cc_final: 0.6923 (mttm) REVERT: U 193 ASP cc_start: 0.7637 (t0) cc_final: 0.7239 (t0) REVERT: U 228 GLU cc_start: 0.7519 (mm-30) cc_final: 0.6735 (mm-30) REVERT: U 230 GLN cc_start: 0.8239 (tt0) cc_final: 0.7993 (tt0) REVERT: U 233 LYS cc_start: 0.7313 (mmmt) cc_final: 0.6836 (mmmt) REVERT: U 264 GLU cc_start: 0.8095 (mt-10) cc_final: 0.6906 (mt-10) REVERT: U 281 LYS cc_start: 0.7932 (ttmm) cc_final: 0.7571 (tttp) REVERT: U 282 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7004 (mt-10) REVERT: U 322 MET cc_start: 0.7824 (mtt) cc_final: 0.7597 (mtm) REVERT: U 339 SER cc_start: 0.8242 (m) cc_final: 0.8014 (t) REVERT: U 374 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7412 (mm-30) REVERT: U 385 ASP cc_start: 0.7414 (m-30) cc_final: 0.7176 (m-30) REVERT: U 438 LYS cc_start: 0.7477 (ttpp) cc_final: 0.6899 (tppt) REVERT: U 451 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7196 (mp10) REVERT: V 36 ASP cc_start: 0.7038 (m-30) cc_final: 0.6485 (m-30) REVERT: V 37 GLU cc_start: 0.7610 (mp0) cc_final: 0.7283 (mp0) REVERT: V 40 VAL cc_start: 0.7421 (t) cc_final: 0.6751 (t) REVERT: V 42 LYS cc_start: 0.7190 (mtmm) cc_final: 0.6413 (tttt) REVERT: V 69 LYS cc_start: 0.7792 (mttm) cc_final: 0.7311 (mtmm) REVERT: V 99 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7684 (mtpt) REVERT: V 135 GLU cc_start: 0.7437 (tt0) cc_final: 0.7156 (tt0) REVERT: V 177 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7714 (ttpp) REVERT: V 178 THR cc_start: 0.8156 (m) cc_final: 0.7769 (p) REVERT: V 180 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7542 (ttp80) REVERT: V 182 ASP cc_start: 0.7502 (p0) cc_final: 0.7238 (p0) REVERT: V 187 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6625 (mm-30) REVERT: V 193 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7448 (mtpt) REVERT: V 203 GLU cc_start: 0.7717 (pt0) cc_final: 0.7415 (mt-10) REVERT: V 214 ARG cc_start: 0.7269 (mmt180) cc_final: 0.6910 (mmm-85) REVERT: V 227 GLU cc_start: 0.7551 (tt0) cc_final: 0.7204 (mm-30) REVERT: V 294 LYS cc_start: 0.7575 (tppt) cc_final: 0.7328 (tppt) REVERT: V 297 ASP cc_start: 0.7796 (t0) cc_final: 0.7441 (t0) REVERT: V 302 GLU cc_start: 0.7140 (pt0) cc_final: 0.6868 (pt0) REVERT: V 326 LYS cc_start: 0.7564 (tmmt) cc_final: 0.7172 (tppt) REVERT: V 355 SER cc_start: 0.8196 (m) cc_final: 0.7745 (t) REVERT: V 392 ARG cc_start: 0.8130 (mtt-85) cc_final: 0.7704 (mtt-85) REVERT: V 454 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7843 (ttmm) REVERT: W 38 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7278 (mtt90) REVERT: W 113 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7542 (mtmm) REVERT: W 146 ASP cc_start: 0.8488 (m-30) cc_final: 0.8187 (m-30) REVERT: W 154 LYS cc_start: 0.8308 (mtpp) cc_final: 0.8099 (mtmt) REVERT: W 167 THR cc_start: 0.8001 (p) cc_final: 0.7710 (t) REVERT: W 170 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7485 (mt-10) REVERT: W 193 ASP cc_start: 0.7504 (t0) cc_final: 0.7165 (t0) REVERT: W 266 ARG cc_start: 0.7176 (mtm-85) cc_final: 0.6623 (mtm-85) REVERT: W 285 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7975 (ttmm) REVERT: W 302 ASP cc_start: 0.7332 (t0) cc_final: 0.6755 (t0) REVERT: W 304 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6677 (mp0) REVERT: W 322 MET cc_start: 0.8118 (ttm) cc_final: 0.7860 (ttm) REVERT: W 333 ARG cc_start: 0.8066 (mtm180) cc_final: 0.7794 (mtm180) REVERT: W 338 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7820 (mtmm) REVERT: W 357 LYS cc_start: 0.7783 (pptt) cc_final: 0.7231 (pptt) REVERT: W 360 ASN cc_start: 0.7153 (m-40) cc_final: 0.6932 (m-40) REVERT: W 378 GLU cc_start: 0.7774 (mp0) cc_final: 0.7100 (tm-30) REVERT: W 385 ASP cc_start: 0.7815 (m-30) cc_final: 0.7456 (m-30) REVERT: W 388 THR cc_start: 0.8140 (m) cc_final: 0.7874 (p) REVERT: W 393 GLU cc_start: 0.7890 (tt0) cc_final: 0.7389 (mt-10) REVERT: W 413 ARG cc_start: 0.7633 (mtp180) cc_final: 0.7185 (mtm180) REVERT: W 438 LYS cc_start: 0.7963 (tppp) cc_final: 0.7504 (tppp) REVERT: W 443 ASN cc_start: 0.6709 (m110) cc_final: 0.6432 (m-40) REVERT: W 449 ASP cc_start: 0.7277 (t70) cc_final: 0.6888 (t70) REVERT: W 451 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7534 (mm110) REVERT: X 75 ILE cc_start: 0.7835 (mt) cc_final: 0.7534 (tt) REVERT: X 77 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6382 (pt) REVERT: X 100 VAL cc_start: 0.8139 (t) cc_final: 0.7907 (m) REVERT: X 132 ARG cc_start: 0.7913 (tpp80) cc_final: 0.7393 (ttm-80) REVERT: X 144 VAL cc_start: 0.8408 (t) cc_final: 0.8159 (p) REVERT: X 177 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7877 (ttmm) REVERT: X 187 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7421 (mm-30) REVERT: X 192 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7260 (mt-10) REVERT: X 201 TYR cc_start: 0.8015 (t80) cc_final: 0.7078 (t80) REVERT: X 210 LYS cc_start: 0.7301 (ptmt) cc_final: 0.6839 (ptmt) REVERT: X 211 ARG cc_start: 0.7479 (mtp-110) cc_final: 0.7207 (mtp180) REVERT: X 221 GLU cc_start: 0.7637 (tp30) cc_final: 0.7432 (pt0) REVERT: X 226 THR cc_start: 0.7374 (OUTLIER) cc_final: 0.7124 (p) REVERT: X 227 GLU cc_start: 0.6033 (tt0) cc_final: 0.5756 (tm-30) REVERT: X 228 GLU cc_start: 0.6590 (pt0) cc_final: 0.5778 (pt0) REVERT: X 282 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6540 (tm-30) REVERT: X 295 TYR cc_start: 0.7838 (m-80) cc_final: 0.7133 (m-80) REVERT: X 315 MET cc_start: 0.7771 (mmp) cc_final: 0.7465 (mmm) REVERT: X 317 ASP cc_start: 0.6677 (OUTLIER) cc_final: 0.6220 (p0) REVERT: X 409 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7379 (tm-30) REVERT: X 432 LYS cc_start: 0.8286 (mmmt) cc_final: 0.7761 (mmmm) REVERT: X 434 ILE cc_start: 0.7366 (mt) cc_final: 0.7051 (tt) REVERT: Y 60 MET cc_start: 0.7732 (ttm) cc_final: 0.7395 (ttm) REVERT: Y 107 PHE cc_start: 0.8257 (m-80) cc_final: 0.7892 (m-80) REVERT: Y 115 GLU cc_start: 0.6844 (tm-30) cc_final: 0.6258 (tm-30) REVERT: Y 142 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7517 (mt-10) REVERT: Y 144 GLN cc_start: 0.6782 (tt0) cc_final: 0.6303 (tt0) REVERT: Y 159 THR cc_start: 0.7854 (m) cc_final: 0.7403 (p) REVERT: Y 188 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: Y 194 LYS cc_start: 0.7298 (mttt) cc_final: 0.7090 (mttt) REVERT: Y 206 PHE cc_start: 0.7830 (m-80) cc_final: 0.7609 (m-80) REVERT: Y 210 ARG cc_start: 0.7980 (mmm160) cc_final: 0.7432 (mmm160) REVERT: Y 232 ARG cc_start: 0.7485 (ttm110) cc_final: 0.7184 (ttm110) REVERT: Y 264 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7770 (mt-10) REVERT: Y 283 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6666 (mt-10) REVERT: Y 316 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6976 (mt-10) REVERT: Y 317 PHE cc_start: 0.8518 (m-80) cc_final: 0.8229 (m-80) REVERT: Y 357 LYS cc_start: 0.7911 (mttm) cc_final: 0.7584 (mmtp) REVERT: Y 359 TYR cc_start: 0.7939 (m-80) cc_final: 0.7731 (m-80) REVERT: Y 378 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6793 (mm-30) REVERT: Y 443 ASN cc_start: 0.7560 (m110) cc_final: 0.7147 (m110) REVERT: Y 444 GLU cc_start: 0.7568 (tt0) cc_final: 0.6993 (tp30) REVERT: Y 449 ASP cc_start: 0.7546 (t70) cc_final: 0.7067 (m-30) REVERT: Y 453 ASN cc_start: 0.8071 (m110) cc_final: 0.7502 (m-40) REVERT: Z 311 ARG cc_start: 0.7900 (ttm110) cc_final: 0.7402 (mtp85) REVERT: Z 312 TYR cc_start: 0.7936 (m-80) cc_final: 0.7669 (m-80) outliers start: 87 outliers final: 44 residues processed: 985 average time/residue: 0.4715 time to fit residues: 700.4504 Evaluate side-chains 943 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 892 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1001 ILE Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1243 SER Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 134 LYS Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 314 ASN Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 168 ILE Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 188 ASP Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Y residue 458 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 272 optimal weight: 4.9990 chunk 223 optimal weight: 0.6980 chunk 90 optimal weight: 0.0040 chunk 328 optimal weight: 6.9990 chunk 354 optimal weight: 2.9990 chunk 292 optimal weight: 0.8980 chunk 325 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS R 144 GLN R 601 HIS R 613 HIS R 659 GLN R 749 ASN ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 ASN T 437 ASN ** V 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN V 427 GLN W 144 GLN W 155 GLN X 331 ASN Y 25 HIS Y 230 GLN Y 415 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29102 Z= 0.273 Angle : 0.573 7.442 39373 Z= 0.285 Chirality : 0.044 0.179 4620 Planarity : 0.004 0.051 5040 Dihedral : 6.811 143.554 4005 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.45 % Allowed : 24.11 % Favored : 72.45 % 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: -0.23 (0.14), residues: 3618 helix: 0.40 (0.14), residues: 1480 sheet: 0.63 (0.20), residues: 649 loop : -1.02 (0.15), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q1361 HIS 0.022 0.001 HIS R 121 PHE 0.022 0.002 PHE R 70 TYR 0.016 0.002 TYR T 201 ARG 0.010 0.000 ARG V 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 942 time to evaluate : 3.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7117 (p0) REVERT: Q 1112 LYS cc_start: 0.8326 (mtpp) cc_final: 0.7960 (mtpp) REVERT: Q 1189 SER cc_start: 0.7902 (t) cc_final: 0.7493 (p) REVERT: Q 1199 GLU cc_start: 0.7326 (pt0) cc_final: 0.7063 (pt0) REVERT: Q 1208 ARG cc_start: 0.7899 (ttm170) cc_final: 0.7613 (ptm160) REVERT: Q 1255 TYR cc_start: 0.7684 (t80) cc_final: 0.7148 (t80) REVERT: Q 1287 SER cc_start: 0.7981 (m) cc_final: 0.7551 (t) REVERT: Q 1316 HIS cc_start: 0.7699 (m-70) cc_final: 0.6887 (m-70) REVERT: Q 1327 MET cc_start: 0.6001 (mmm) cc_final: 0.5740 (mmm) REVERT: Q 1361 TRP cc_start: 0.7413 (OUTLIER) cc_final: 0.6974 (t60) REVERT: Q 1432 MET cc_start: 0.4485 (tpp) cc_final: 0.3870 (tpp) REVERT: R 65 ASN cc_start: 0.8253 (t0) cc_final: 0.7978 (t0) REVERT: R 79 PHE cc_start: 0.8044 (m-10) cc_final: 0.7810 (m-10) REVERT: R 85 ASP cc_start: 0.8825 (m-30) cc_final: 0.8563 (m-30) REVERT: R 93 ARG cc_start: 0.8551 (tmm-80) cc_final: 0.8147 (ttp-170) REVERT: R 95 GLN cc_start: 0.8938 (mt0) cc_final: 0.8637 (mt0) REVERT: R 97 ARG cc_start: 0.7884 (ttp-110) cc_final: 0.7636 (ttp-110) REVERT: R 146 GLN cc_start: 0.7612 (tt0) cc_final: 0.7264 (tt0) REVERT: R 192 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7340 (mm-30) REVERT: R 242 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7301 (mt0) REVERT: R 244 GLU cc_start: 0.7692 (tt0) cc_final: 0.7239 (tt0) REVERT: R 257 TYR cc_start: 0.7978 (t80) cc_final: 0.7767 (t80) REVERT: R 258 ASP cc_start: 0.8187 (m-30) cc_final: 0.7913 (m-30) REVERT: R 260 ASP cc_start: 0.7504 (m-30) cc_final: 0.7092 (m-30) REVERT: R 262 GLU cc_start: 0.7759 (mp0) cc_final: 0.7090 (mp0) REVERT: R 264 ILE cc_start: 0.8357 (tt) cc_final: 0.7999 (tp) REVERT: R 269 ASN cc_start: 0.7225 (t0) cc_final: 0.6617 (t0) REVERT: R 596 ARG cc_start: 0.8318 (mpt180) cc_final: 0.8073 (mmt-90) REVERT: R 677 VAL cc_start: 0.8680 (t) cc_final: 0.8405 (m) REVERT: R 709 ASP cc_start: 0.7421 (m-30) cc_final: 0.7126 (m-30) REVERT: R 720 ASN cc_start: 0.7642 (t0) cc_final: 0.6641 (t0) REVERT: R 723 GLN cc_start: 0.7638 (mp10) cc_final: 0.6716 (mp10) REVERT: R 724 TYR cc_start: 0.7831 (t80) cc_final: 0.7397 (t80) REVERT: R 726 LYS cc_start: 0.8358 (mptt) cc_final: 0.8117 (mtmm) REVERT: R 735 GLU cc_start: 0.8268 (mp0) cc_final: 0.8040 (mp0) REVERT: R 736 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7144 (tm-30) REVERT: S 114 LYS cc_start: 0.7886 (mttp) cc_final: 0.7562 (mttp) REVERT: S 127 SER cc_start: 0.8378 (t) cc_final: 0.7994 (t) REVERT: T 99 LYS cc_start: 0.8113 (ttpp) cc_final: 0.7877 (ttpp) REVERT: T 105 LEU cc_start: 0.8127 (tp) cc_final: 0.7824 (tp) REVERT: T 122 MET cc_start: 0.7417 (tpt) cc_final: 0.7185 (mmm) REVERT: T 123 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7024 (mt-10) REVERT: T 134 LYS cc_start: 0.8466 (mtpp) cc_final: 0.8123 (mtmm) REVERT: T 195 SER cc_start: 0.7957 (m) cc_final: 0.7673 (t) REVERT: T 276 LYS cc_start: 0.7930 (pttt) cc_final: 0.7705 (pttt) REVERT: T 295 TYR cc_start: 0.7698 (m-80) cc_final: 0.7370 (m-80) REVERT: T 317 ASP cc_start: 0.7462 (t0) cc_final: 0.7177 (t0) REVERT: T 365 ASP cc_start: 0.7731 (m-30) cc_final: 0.7307 (m-30) REVERT: T 385 GLU cc_start: 0.7686 (tt0) cc_final: 0.7387 (tm-30) REVERT: T 441 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7206 (tp30) REVERT: U 65 THR cc_start: 0.7422 (p) cc_final: 0.7174 (t) REVERT: U 105 GLU cc_start: 0.7969 (tt0) cc_final: 0.7690 (tt0) REVERT: U 107 PHE cc_start: 0.8544 (m-80) cc_final: 0.8035 (m-80) REVERT: U 131 GLU cc_start: 0.7048 (pt0) cc_final: 0.6764 (pt0) REVERT: U 139 GLU cc_start: 0.8008 (tt0) cc_final: 0.7724 (tt0) REVERT: U 142 GLU cc_start: 0.6782 (tm-30) cc_final: 0.6042 (tm-30) REVERT: U 144 GLN cc_start: 0.6725 (OUTLIER) cc_final: 0.5789 (mp10) REVERT: U 157 LYS cc_start: 0.7677 (mttt) cc_final: 0.6895 (mttm) REVERT: U 170 GLU cc_start: 0.7192 (tp30) cc_final: 0.6943 (tp30) REVERT: U 193 ASP cc_start: 0.7723 (t0) cc_final: 0.7167 (t0) REVERT: U 228 GLU cc_start: 0.7577 (mm-30) cc_final: 0.6782 (mm-30) REVERT: U 233 LYS cc_start: 0.7324 (mmmt) cc_final: 0.6848 (mmmt) REVERT: U 264 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7139 (tt0) REVERT: U 281 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7634 (tttp) REVERT: U 282 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7130 (mt-10) REVERT: U 283 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6729 (mt-10) REVERT: U 296 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7828 (m-30) REVERT: U 316 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: U 339 SER cc_start: 0.8271 (m) cc_final: 0.8062 (t) REVERT: U 374 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7404 (mm-30) REVERT: U 376 GLU cc_start: 0.7351 (pm20) cc_final: 0.7148 (pm20) REVERT: U 385 ASP cc_start: 0.7374 (m-30) cc_final: 0.7149 (m-30) REVERT: U 438 LYS cc_start: 0.7475 (ttpp) cc_final: 0.7098 (tppt) REVERT: U 439 TYR cc_start: 0.7143 (m-80) cc_final: 0.6849 (m-80) REVERT: U 451 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7086 (mp10) REVERT: V 36 ASP cc_start: 0.6996 (m-30) cc_final: 0.6630 (m-30) REVERT: V 40 VAL cc_start: 0.7560 (t) cc_final: 0.6964 (t) REVERT: V 42 LYS cc_start: 0.7277 (mtmm) cc_final: 0.6424 (tttt) REVERT: V 69 LYS cc_start: 0.7853 (mttm) cc_final: 0.7340 (mtmm) REVERT: V 99 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7721 (mtpt) REVERT: V 135 GLU cc_start: 0.7473 (tt0) cc_final: 0.7250 (tt0) REVERT: V 177 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7631 (ttpp) REVERT: V 178 THR cc_start: 0.8113 (m) cc_final: 0.7713 (p) REVERT: V 193 LYS cc_start: 0.7742 (mtpt) cc_final: 0.7497 (mtpt) REVERT: V 195 SER cc_start: 0.7935 (OUTLIER) cc_final: 0.7599 (p) REVERT: V 203 GLU cc_start: 0.7597 (pt0) cc_final: 0.7362 (mt-10) REVERT: V 214 ARG cc_start: 0.7307 (mmt180) cc_final: 0.6659 (mmm-85) REVERT: V 227 GLU cc_start: 0.7538 (tt0) cc_final: 0.7173 (mm-30) REVERT: V 294 LYS cc_start: 0.7540 (tppt) cc_final: 0.7293 (tppt) REVERT: V 297 ASP cc_start: 0.7797 (t0) cc_final: 0.7458 (t0) REVERT: V 302 GLU cc_start: 0.7178 (pt0) cc_final: 0.6881 (pt0) REVERT: V 326 LYS cc_start: 0.7502 (tmmt) cc_final: 0.7129 (tppt) REVERT: V 355 SER cc_start: 0.8229 (m) cc_final: 0.7721 (t) REVERT: V 365 ASP cc_start: 0.7930 (m-30) cc_final: 0.7140 (t0) REVERT: V 392 ARG cc_start: 0.8147 (mtt-85) cc_final: 0.7724 (mtt-85) REVERT: V 394 GLN cc_start: 0.7666 (mt0) cc_final: 0.7424 (pt0) REVERT: V 406 MET cc_start: 0.6391 (mmt) cc_final: 0.6172 (mtt) REVERT: V 454 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7905 (ttmm) REVERT: W 38 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.7196 (mtt90) REVERT: W 130 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7616 (ttmm) REVERT: W 146 ASP cc_start: 0.8557 (m-30) cc_final: 0.8178 (m-30) REVERT: W 161 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7683 (pttp) REVERT: W 167 THR cc_start: 0.8027 (p) cc_final: 0.7753 (t) REVERT: W 170 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7514 (mt-10) REVERT: W 181 LYS cc_start: 0.7534 (ttpp) cc_final: 0.7323 (ttpp) REVERT: W 182 GLU cc_start: 0.7768 (tt0) cc_final: 0.7209 (tm-30) REVERT: W 189 VAL cc_start: 0.7372 (p) cc_final: 0.7086 (m) REVERT: W 193 ASP cc_start: 0.7526 (t0) cc_final: 0.7177 (t0) REVERT: W 204 ARG cc_start: 0.7109 (ttt90) cc_final: 0.6583 (ttt90) REVERT: W 266 ARG cc_start: 0.7178 (mtm-85) cc_final: 0.6592 (mtm-85) REVERT: W 285 LYS cc_start: 0.8191 (ttmm) cc_final: 0.7977 (ttmm) REVERT: W 302 ASP cc_start: 0.7333 (t0) cc_final: 0.6841 (t0) REVERT: W 304 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6730 (mp0) REVERT: W 333 ARG cc_start: 0.8047 (mtm180) cc_final: 0.7826 (mtm180) REVERT: W 338 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7921 (mtmt) REVERT: W 376 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: W 378 GLU cc_start: 0.7843 (mp0) cc_final: 0.7130 (tm-30) REVERT: W 385 ASP cc_start: 0.7815 (m-30) cc_final: 0.7412 (m-30) REVERT: W 388 THR cc_start: 0.8233 (m) cc_final: 0.7962 (p) REVERT: W 389 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7646 (mtmm) REVERT: W 393 GLU cc_start: 0.7936 (tt0) cc_final: 0.7449 (mt-10) REVERT: W 413 ARG cc_start: 0.7624 (mtp180) cc_final: 0.7166 (mtm180) REVERT: W 438 LYS cc_start: 0.7850 (tppp) cc_final: 0.7568 (tppp) REVERT: W 443 ASN cc_start: 0.6860 (m110) cc_final: 0.6533 (m-40) REVERT: W 449 ASP cc_start: 0.7343 (t70) cc_final: 0.6973 (t70) REVERT: W 451 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7506 (mm110) REVERT: X 77 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6481 (pp) REVERT: X 132 ARG cc_start: 0.7914 (tpp80) cc_final: 0.7307 (ttm-80) REVERT: X 143 GLU cc_start: 0.7623 (tt0) cc_final: 0.7368 (tt0) REVERT: X 171 LYS cc_start: 0.7840 (tttt) cc_final: 0.7596 (tppt) REVERT: X 187 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7482 (mm-30) REVERT: X 201 TYR cc_start: 0.7975 (t80) cc_final: 0.7221 (t80) REVERT: X 210 LYS cc_start: 0.7382 (ptmt) cc_final: 0.6863 (ptmt) REVERT: X 211 ARG cc_start: 0.7782 (mtp-110) cc_final: 0.7219 (mtp180) REVERT: X 221 GLU cc_start: 0.7709 (tp30) cc_final: 0.7325 (tt0) REVERT: X 226 THR cc_start: 0.7522 (OUTLIER) cc_final: 0.7301 (p) REVERT: X 228 GLU cc_start: 0.6693 (pt0) cc_final: 0.6328 (pt0) REVERT: X 276 LYS cc_start: 0.7605 (tttm) cc_final: 0.7150 (tmtt) REVERT: X 282 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6270 (tp30) REVERT: X 290 LYS cc_start: 0.7664 (ttmm) cc_final: 0.7306 (mtmt) REVERT: X 295 TYR cc_start: 0.7985 (m-80) cc_final: 0.7735 (m-80) REVERT: X 315 MET cc_start: 0.7928 (mmp) cc_final: 0.7576 (mmm) REVERT: X 317 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6301 (p0) REVERT: X 432 LYS cc_start: 0.8411 (mmmt) cc_final: 0.8138 (mmmm) REVERT: X 434 ILE cc_start: 0.7293 (mt) cc_final: 0.6964 (tt) REVERT: X 438 ASP cc_start: 0.7895 (m-30) cc_final: 0.7637 (m-30) REVERT: Y 60 MET cc_start: 0.7768 (ttm) cc_final: 0.7486 (ttm) REVERT: Y 90 GLN cc_start: 0.7336 (mm-40) cc_final: 0.7088 (mm110) REVERT: Y 132 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7833 (mp0) REVERT: Y 144 GLN cc_start: 0.6745 (tt0) cc_final: 0.6233 (tt0) REVERT: Y 194 LYS cc_start: 0.7206 (mttt) cc_final: 0.6859 (mttt) REVERT: Y 210 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7524 (mmm160) REVERT: Y 283 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6745 (mt-10) REVERT: Y 314 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7715 (mp0) REVERT: Y 317 PHE cc_start: 0.8580 (m-80) cc_final: 0.8262 (m-80) REVERT: Y 357 LYS cc_start: 0.8064 (mttm) cc_final: 0.7786 (mmtp) REVERT: Y 361 GLU cc_start: 0.7259 (tt0) cc_final: 0.6937 (tp30) REVERT: Y 378 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6736 (mm-30) REVERT: Y 415 ASN cc_start: 0.7378 (t0) cc_final: 0.6775 (t0) REVERT: Y 443 ASN cc_start: 0.7528 (m110) cc_final: 0.7147 (m110) REVERT: Y 444 GLU cc_start: 0.7579 (tt0) cc_final: 0.7026 (tp30) REVERT: Y 449 ASP cc_start: 0.7567 (t70) cc_final: 0.7042 (m-30) REVERT: Y 453 ASN cc_start: 0.7969 (m110) cc_final: 0.7522 (m-40) REVERT: Z 311 ARG cc_start: 0.7933 (ttm110) cc_final: 0.7432 (mtp85) REVERT: Z 312 TYR cc_start: 0.7965 (m-80) cc_final: 0.7622 (m-80) outliers start: 109 outliers final: 69 residues processed: 997 average time/residue: 0.4497 time to fit residues: 677.7682 Evaluate side-chains 979 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 896 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1001 ILE Chi-restraints excluded: chain Q residue 1103 ASP Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1243 SER Chi-restraints excluded: chain Q residue 1267 ASP Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 617 GLU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 314 ASN Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain T residue 448 ASP Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 261 ASP Chi-restraints excluded: chain U residue 296 ASP Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 316 GLU Chi-restraints excluded: chain U residue 346 ASP Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 448 ILE Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 195 SER Chi-restraints excluded: chain V residue 314 ASN Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain V residue 458 THR Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 130 LYS Chi-restraints excluded: chain W residue 161 LYS Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 182 ASP Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 264 ASP Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 391 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 418 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 36 optimal weight: 0.0570 chunk 156 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 329 optimal weight: 2.9990 chunk 348 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 312 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 107 ASN R 121 HIS R 144 GLN R 613 HIS ** R 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 256 ASN T 440 ASN U 230 GLN U 272 GLN V 325 ASN W 90 GLN W 144 GLN W 360 ASN X 256 ASN X 325 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 29102 Z= 0.338 Angle : 0.609 7.573 39373 Z= 0.303 Chirality : 0.046 0.183 4620 Planarity : 0.004 0.056 5040 Dihedral : 6.823 143.313 4005 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.56 % Allowed : 24.01 % Favored : 71.43 % 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: -0.14 (0.14), residues: 3618 helix: 0.54 (0.14), residues: 1475 sheet: 0.54 (0.19), residues: 667 loop : -0.97 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q1361 HIS 0.008 0.001 HIS V 165 PHE 0.018 0.002 PHE R 753 TYR 0.020 0.002 TYR T 201 ARG 0.012 0.000 ARG V 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 942 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7073 (p0) REVERT: Q 1112 LYS cc_start: 0.8287 (mtpp) cc_final: 0.7913 (mtpp) REVERT: Q 1134 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7547 (mm-30) REVERT: Q 1139 GLU cc_start: 0.7153 (tp30) cc_final: 0.6019 (tp30) REVERT: Q 1142 ARG cc_start: 0.7180 (ttp-110) cc_final: 0.6883 (ptp90) REVERT: Q 1189 SER cc_start: 0.7862 (t) cc_final: 0.7473 (p) REVERT: Q 1199 GLU cc_start: 0.7174 (pt0) cc_final: 0.6709 (pm20) REVERT: Q 1208 ARG cc_start: 0.7919 (ttm170) cc_final: 0.7395 (tpp80) REVERT: Q 1255 TYR cc_start: 0.7662 (t80) cc_final: 0.7297 (t80) REVERT: Q 1287 SER cc_start: 0.8027 (m) cc_final: 0.7545 (t) REVERT: Q 1291 MET cc_start: 0.7566 (tpp) cc_final: 0.7341 (tpp) REVERT: Q 1316 HIS cc_start: 0.7706 (m-70) cc_final: 0.6932 (m-70) REVERT: Q 1327 MET cc_start: 0.6126 (mmm) cc_final: 0.5897 (mmm) REVERT: Q 1331 MET cc_start: 0.7467 (mmm) cc_final: 0.7150 (mmm) REVERT: Q 1432 MET cc_start: 0.4533 (tpp) cc_final: 0.3945 (tpp) REVERT: R 65 ASN cc_start: 0.8308 (t0) cc_final: 0.8034 (t0) REVERT: R 79 PHE cc_start: 0.8070 (m-10) cc_final: 0.7790 (m-10) REVERT: R 85 ASP cc_start: 0.8822 (m-30) cc_final: 0.8558 (m-30) REVERT: R 93 ARG cc_start: 0.8573 (tmm-80) cc_final: 0.8120 (ttp-170) REVERT: R 95 GLN cc_start: 0.8928 (mt0) cc_final: 0.8611 (mt0) REVERT: R 97 ARG cc_start: 0.7853 (ttp-110) cc_final: 0.7623 (ttp-110) REVERT: R 144 GLN cc_start: 0.6873 (pt0) cc_final: 0.6604 (pt0) REVERT: R 146 GLN cc_start: 0.7590 (tt0) cc_final: 0.7377 (mm-40) REVERT: R 176 TYR cc_start: 0.8441 (m-80) cc_final: 0.8239 (m-80) REVERT: R 192 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7349 (mm-30) REVERT: R 227 MET cc_start: 0.8363 (mmp) cc_final: 0.8060 (mmm) REVERT: R 242 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7311 (mt0) REVERT: R 244 GLU cc_start: 0.7682 (tt0) cc_final: 0.7389 (tt0) REVERT: R 249 ASP cc_start: 0.8106 (m-30) cc_final: 0.7855 (m-30) REVERT: R 258 ASP cc_start: 0.8275 (m-30) cc_final: 0.8049 (m-30) REVERT: R 260 ASP cc_start: 0.7501 (m-30) cc_final: 0.7069 (m-30) REVERT: R 262 GLU cc_start: 0.7729 (mp0) cc_final: 0.7090 (mp0) REVERT: R 264 ILE cc_start: 0.8262 (tt) cc_final: 0.7851 (tp) REVERT: R 269 ASN cc_start: 0.7196 (t0) cc_final: 0.6642 (t0) REVERT: R 270 LEU cc_start: 0.8351 (mt) cc_final: 0.8126 (mm) REVERT: R 608 GLU cc_start: 0.7799 (mt-10) cc_final: 0.6887 (tt0) REVERT: R 617 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: R 677 VAL cc_start: 0.8710 (t) cc_final: 0.8403 (m) REVERT: R 709 ASP cc_start: 0.7544 (m-30) cc_final: 0.7251 (m-30) REVERT: R 720 ASN cc_start: 0.7710 (t0) cc_final: 0.6806 (t0) REVERT: R 723 GLN cc_start: 0.7669 (mp10) cc_final: 0.6728 (mp10) REVERT: R 724 TYR cc_start: 0.7847 (t80) cc_final: 0.7408 (t80) REVERT: R 726 LYS cc_start: 0.8402 (mptt) cc_final: 0.8152 (mtmm) REVERT: R 736 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7125 (tm-30) REVERT: R 744 GLU cc_start: 0.7921 (tp30) cc_final: 0.7524 (tp30) REVERT: S 114 LYS cc_start: 0.7900 (mttp) cc_final: 0.7612 (mttp) REVERT: S 127 SER cc_start: 0.8408 (t) cc_final: 0.8076 (t) REVERT: T 24 THR cc_start: 0.7893 (m) cc_final: 0.7651 (p) REVERT: T 99 LYS cc_start: 0.8111 (ttpp) cc_final: 0.7651 (ttmm) REVERT: T 105 LEU cc_start: 0.8106 (tp) cc_final: 0.7745 (tp) REVERT: T 122 MET cc_start: 0.7411 (tpt) cc_final: 0.7187 (mmm) REVERT: T 123 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7033 (mt-10) REVERT: T 134 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8096 (mtmm) REVERT: T 182 ASP cc_start: 0.6731 (OUTLIER) cc_final: 0.6526 (p0) REVERT: T 195 SER cc_start: 0.7878 (m) cc_final: 0.7623 (t) REVERT: T 295 TYR cc_start: 0.7725 (m-80) cc_final: 0.7369 (m-80) REVERT: T 317 ASP cc_start: 0.7437 (t0) cc_final: 0.7143 (t0) REVERT: T 331 ASN cc_start: 0.8044 (m-40) cc_final: 0.7665 (m110) REVERT: T 362 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: T 365 ASP cc_start: 0.7787 (m-30) cc_final: 0.7347 (m-30) REVERT: T 385 GLU cc_start: 0.7709 (tt0) cc_final: 0.7360 (tm-30) REVERT: T 392 ARG cc_start: 0.7507 (mtm110) cc_final: 0.7189 (mtm110) REVERT: T 441 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7219 (tp30) REVERT: U 65 THR cc_start: 0.7495 (p) cc_final: 0.7180 (t) REVERT: U 105 GLU cc_start: 0.7971 (tt0) cc_final: 0.7668 (tt0) REVERT: U 107 PHE cc_start: 0.8584 (m-80) cc_final: 0.8106 (m-80) REVERT: U 131 GLU cc_start: 0.6978 (pt0) cc_final: 0.6634 (pt0) REVERT: U 142 GLU cc_start: 0.6680 (tm-30) cc_final: 0.5609 (tm-30) REVERT: U 144 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.5218 (mp10) REVERT: U 157 LYS cc_start: 0.7722 (mttt) cc_final: 0.6640 (mttm) REVERT: U 170 GLU cc_start: 0.7162 (tp30) cc_final: 0.6856 (tp30) REVERT: U 185 LEU cc_start: 0.8053 (mp) cc_final: 0.7752 (mp) REVERT: U 188 ASP cc_start: 0.8039 (m-30) cc_final: 0.7527 (m-30) REVERT: U 193 ASP cc_start: 0.7778 (t0) cc_final: 0.7241 (t0) REVERT: U 228 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7235 (mm-30) REVERT: U 233 LYS cc_start: 0.7291 (mmmt) cc_final: 0.6872 (mmmt) REVERT: U 264 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7658 (tt0) REVERT: U 281 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7735 (tttp) REVERT: U 282 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7226 (mt-10) REVERT: U 283 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6851 (mt-10) REVERT: U 339 SER cc_start: 0.8312 (m) cc_final: 0.8106 (t) REVERT: U 374 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7349 (mm-30) REVERT: U 381 SER cc_start: 0.6710 (p) cc_final: 0.6366 (m) REVERT: U 439 TYR cc_start: 0.6979 (m-80) cc_final: 0.6726 (m-80) REVERT: U 451 GLN cc_start: 0.7408 (mm-40) cc_final: 0.7048 (mm-40) REVERT: V 36 ASP cc_start: 0.6915 (m-30) cc_final: 0.6560 (m-30) REVERT: V 40 VAL cc_start: 0.7648 (t) cc_final: 0.7110 (t) REVERT: V 42 LYS cc_start: 0.7307 (mtmm) cc_final: 0.6353 (tttm) REVERT: V 69 LYS cc_start: 0.7921 (mttm) cc_final: 0.7368 (mtmm) REVERT: V 99 LYS cc_start: 0.8271 (mtpt) cc_final: 0.7804 (mtpt) REVERT: V 109 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7755 (mt-10) REVERT: V 135 GLU cc_start: 0.7475 (tt0) cc_final: 0.7207 (tt0) REVERT: V 177 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7649 (ttpp) REVERT: V 178 THR cc_start: 0.8042 (m) cc_final: 0.7642 (p) REVERT: V 190 GLN cc_start: 0.7581 (tm-30) cc_final: 0.7320 (tm-30) REVERT: V 193 LYS cc_start: 0.7801 (mtpt) cc_final: 0.7561 (mtpt) REVERT: V 198 ASP cc_start: 0.7336 (m-30) cc_final: 0.6855 (m-30) REVERT: V 214 ARG cc_start: 0.7290 (mmt180) cc_final: 0.6634 (mmm-85) REVERT: V 216 ASP cc_start: 0.7197 (p0) cc_final: 0.6982 (p0) REVERT: V 227 GLU cc_start: 0.7533 (tt0) cc_final: 0.7128 (mm-30) REVERT: V 294 LYS cc_start: 0.7508 (tppt) cc_final: 0.7273 (tppt) REVERT: V 297 ASP cc_start: 0.7796 (t0) cc_final: 0.7467 (t0) REVERT: V 302 GLU cc_start: 0.7163 (pt0) cc_final: 0.6870 (pt0) REVERT: V 326 LYS cc_start: 0.7470 (tmmt) cc_final: 0.7097 (ttmt) REVERT: V 355 SER cc_start: 0.8178 (m) cc_final: 0.7668 (t) REVERT: V 365 ASP cc_start: 0.7905 (m-30) cc_final: 0.7199 (t0) REVERT: V 385 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7109 (mm-30) REVERT: V 394 GLN cc_start: 0.7731 (mt0) cc_final: 0.7414 (pt0) REVERT: V 454 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7871 (ttmm) REVERT: W 38 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.6849 (mtt90) REVERT: W 42 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7537 (mt-10) REVERT: W 167 THR cc_start: 0.8016 (p) cc_final: 0.7754 (t) REVERT: W 170 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7503 (mp0) REVERT: W 181 LYS cc_start: 0.7469 (ttpp) cc_final: 0.7130 (ttpp) REVERT: W 182 GLU cc_start: 0.7863 (tt0) cc_final: 0.7474 (tm-30) REVERT: W 189 VAL cc_start: 0.7366 (p) cc_final: 0.7066 (m) REVERT: W 193 ASP cc_start: 0.7516 (t0) cc_final: 0.7187 (t0) REVERT: W 204 ARG cc_start: 0.7034 (ttt90) cc_final: 0.6544 (ttt90) REVERT: W 257 LEU cc_start: 0.7833 (mt) cc_final: 0.7457 (mt) REVERT: W 266 ARG cc_start: 0.7169 (mtm-85) cc_final: 0.6587 (mtm-85) REVERT: W 304 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6821 (mp0) REVERT: W 331 LYS cc_start: 0.8475 (tttp) cc_final: 0.8233 (mtpp) REVERT: W 338 LYS cc_start: 0.8084 (mtpt) cc_final: 0.7792 (mttm) REVERT: W 376 GLU cc_start: 0.7271 (mp0) cc_final: 0.6941 (mp0) REVERT: W 378 GLU cc_start: 0.7919 (mp0) cc_final: 0.7041 (tm-30) REVERT: W 388 THR cc_start: 0.8232 (m) cc_final: 0.7967 (p) REVERT: W 393 GLU cc_start: 0.7920 (tt0) cc_final: 0.7575 (mt-10) REVERT: W 413 ARG cc_start: 0.7713 (mtp180) cc_final: 0.7284 (mtm180) REVERT: W 432 ASP cc_start: 0.7439 (t70) cc_final: 0.6447 (p0) REVERT: W 438 LYS cc_start: 0.7921 (tppp) cc_final: 0.7586 (tppp) REVERT: W 443 ASN cc_start: 0.6911 (m110) cc_final: 0.6621 (m-40) REVERT: W 449 ASP cc_start: 0.7322 (t70) cc_final: 0.6840 (t0) REVERT: W 451 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7421 (mm110) REVERT: X 75 ILE cc_start: 0.7978 (mt) cc_final: 0.7778 (tt) REVERT: X 77 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6479 (pp) REVERT: X 105 LEU cc_start: 0.7522 (mt) cc_final: 0.7282 (tp) REVERT: X 109 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6442 (mt-10) REVERT: X 114 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7377 (mt-10) REVERT: X 132 ARG cc_start: 0.7878 (tpp80) cc_final: 0.7284 (ttm-80) REVERT: X 143 GLU cc_start: 0.7599 (tt0) cc_final: 0.7307 (tt0) REVERT: X 171 LYS cc_start: 0.7955 (tttt) cc_final: 0.7656 (tppt) REVERT: X 187 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7513 (mm-30) REVERT: X 210 LYS cc_start: 0.7421 (ptmt) cc_final: 0.7147 (ptmt) REVERT: X 211 ARG cc_start: 0.7775 (mtp-110) cc_final: 0.7240 (mtp180) REVERT: X 228 GLU cc_start: 0.6763 (pt0) cc_final: 0.6070 (pt0) REVERT: X 240 LYS cc_start: 0.8401 (mtmt) cc_final: 0.8129 (mtmm) REVERT: X 282 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6333 (tp30) REVERT: X 290 LYS cc_start: 0.7664 (ttmm) cc_final: 0.7292 (mtmt) REVERT: X 315 MET cc_start: 0.8001 (mmp) cc_final: 0.7650 (mmm) REVERT: X 317 ASP cc_start: 0.6744 (OUTLIER) cc_final: 0.6437 (p0) REVERT: X 432 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8245 (mmmm) REVERT: X 434 ILE cc_start: 0.7146 (mt) cc_final: 0.6813 (tt) REVERT: X 438 ASP cc_start: 0.7905 (m-30) cc_final: 0.7678 (m-30) REVERT: Y 132 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7857 (mp0) REVERT: Y 144 GLN cc_start: 0.6741 (tt0) cc_final: 0.6253 (tt0) REVERT: Y 170 GLU cc_start: 0.6478 (mp0) cc_final: 0.6200 (mt-10) REVERT: Y 210 ARG cc_start: 0.8105 (mmm160) cc_final: 0.7646 (mmm160) REVERT: Y 215 MET cc_start: 0.7086 (mtp) cc_final: 0.6761 (mtp) REVERT: Y 228 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7429 (mm-30) REVERT: Y 283 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6895 (mt-10) REVERT: Y 314 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7674 (mp0) REVERT: Y 317 PHE cc_start: 0.8575 (m-80) cc_final: 0.8301 (m-80) REVERT: Y 378 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6732 (mm-30) REVERT: Y 415 ASN cc_start: 0.7364 (t0) cc_final: 0.6902 (t0) REVERT: Y 443 ASN cc_start: 0.7551 (m110) cc_final: 0.7195 (m110) REVERT: Y 444 GLU cc_start: 0.7631 (tt0) cc_final: 0.7064 (tp30) REVERT: Y 449 ASP cc_start: 0.7607 (t70) cc_final: 0.7066 (m-30) REVERT: Y 453 ASN cc_start: 0.7880 (m110) cc_final: 0.7552 (m-40) REVERT: Z 311 ARG cc_start: 0.7923 (ttm110) cc_final: 0.7673 (mtp85) outliers start: 144 outliers final: 92 residues processed: 1019 average time/residue: 0.4470 time to fit residues: 686.0463 Evaluate side-chains 1018 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 916 time to evaluate : 3.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1001 ILE Chi-restraints excluded: chain Q residue 1103 ASP Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1243 SER Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 617 GLU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 246 ASP Chi-restraints excluded: chain T residue 314 ASN Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 362 ASP Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain T residue 438 ASP Chi-restraints excluded: chain T residue 448 ASP Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 32 ASP Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 86 MET Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain U residue 235 VAL Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 346 ASP Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 448 ILE Chi-restraints excluded: chain U residue 458 ILE Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 226 THR Chi-restraints excluded: chain V residue 243 ILE Chi-restraints excluded: chain V residue 274 LYS Chi-restraints excluded: chain V residue 278 THR Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 314 ASN Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain V residue 458 THR Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 109 GLU Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 182 ASP Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 384 LEU Chi-restraints excluded: chain Y residue 418 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 2.9990 chunk 198 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 259 optimal weight: 0.0670 chunk 143 optimal weight: 1.9990 chunk 297 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 178 optimal weight: 0.5980 chunk 313 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 613 HIS R 666 ASN ** R 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 256 ASN T 417 GLN T 440 ASN U 272 GLN ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 256 ASN X 289 ASN X 325 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29102 Z= 0.177 Angle : 0.546 8.878 39373 Z= 0.268 Chirality : 0.043 0.199 4620 Planarity : 0.003 0.042 5040 Dihedral : 6.462 137.677 4004 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.08 % Allowed : 24.80 % Favored : 71.12 % 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 (0.14), residues: 3618 helix: 0.79 (0.14), residues: 1473 sheet: 0.59 (0.20), residues: 664 loop : -0.90 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q1361 HIS 0.024 0.001 HIS R 121 PHE 0.016 0.001 PHE R 691 TYR 0.017 0.001 TYR R 734 ARG 0.009 0.000 ARG Y 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 925 time to evaluate : 3.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7066 (p0) REVERT: Q 1112 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7937 (mtpp) REVERT: Q 1134 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: Q 1139 GLU cc_start: 0.7230 (tp30) cc_final: 0.6042 (tp30) REVERT: Q 1142 ARG cc_start: 0.7185 (ttp-110) cc_final: 0.6895 (ptp90) REVERT: Q 1189 SER cc_start: 0.7902 (t) cc_final: 0.7479 (p) REVERT: Q 1199 GLU cc_start: 0.7082 (pt0) cc_final: 0.6613 (pm20) REVERT: Q 1208 ARG cc_start: 0.7882 (ttm170) cc_final: 0.7471 (tpp80) REVERT: Q 1255 TYR cc_start: 0.7678 (t80) cc_final: 0.7229 (t80) REVERT: Q 1287 SER cc_start: 0.8031 (m) cc_final: 0.7673 (t) REVERT: Q 1316 HIS cc_start: 0.7721 (m-70) cc_final: 0.6911 (m-70) REVERT: Q 1327 MET cc_start: 0.6080 (mmm) cc_final: 0.5852 (mmm) REVERT: Q 1331 MET cc_start: 0.7490 (mmm) cc_final: 0.7238 (mmm) REVERT: Q 1432 MET cc_start: 0.4604 (tpp) cc_final: 0.4037 (tpp) REVERT: R 65 ASN cc_start: 0.8278 (t0) cc_final: 0.8011 (t0) REVERT: R 79 PHE cc_start: 0.8075 (m-10) cc_final: 0.7782 (m-10) REVERT: R 85 ASP cc_start: 0.8815 (m-30) cc_final: 0.8558 (m-30) REVERT: R 93 ARG cc_start: 0.8550 (tmm-80) cc_final: 0.8104 (ttp-170) REVERT: R 95 GLN cc_start: 0.8922 (mt0) cc_final: 0.8602 (mt0) REVERT: R 97 ARG cc_start: 0.7899 (ttp-110) cc_final: 0.7650 (ttp-110) REVERT: R 144 GLN cc_start: 0.6827 (pt0) cc_final: 0.6541 (pt0) REVERT: R 192 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7314 (mm-30) REVERT: R 242 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7400 (mt0) REVERT: R 244 GLU cc_start: 0.7646 (tt0) cc_final: 0.7369 (tt0) REVERT: R 249 ASP cc_start: 0.8184 (m-30) cc_final: 0.7927 (m-30) REVERT: R 260 ASP cc_start: 0.7463 (m-30) cc_final: 0.7023 (m-30) REVERT: R 262 GLU cc_start: 0.7770 (mp0) cc_final: 0.7114 (mp0) REVERT: R 264 ILE cc_start: 0.8201 (tt) cc_final: 0.7771 (tp) REVERT: R 269 ASN cc_start: 0.7172 (t0) cc_final: 0.6619 (t0) REVERT: R 270 LEU cc_start: 0.8367 (mt) cc_final: 0.8147 (mm) REVERT: R 608 GLU cc_start: 0.7687 (mt-10) cc_final: 0.6814 (tt0) REVERT: R 677 VAL cc_start: 0.8687 (t) cc_final: 0.8380 (m) REVERT: R 681 LYS cc_start: 0.7973 (ttpt) cc_final: 0.7764 (ttpp) REVERT: R 709 ASP cc_start: 0.7529 (m-30) cc_final: 0.7228 (m-30) REVERT: R 720 ASN cc_start: 0.7570 (t0) cc_final: 0.6643 (t0) REVERT: R 723 GLN cc_start: 0.7614 (mp10) cc_final: 0.6614 (mp10) REVERT: R 724 TYR cc_start: 0.7791 (t80) cc_final: 0.7348 (t80) REVERT: R 726 LYS cc_start: 0.8325 (mptt) cc_final: 0.8100 (mtmm) REVERT: R 736 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7106 (tm-30) REVERT: S 114 LYS cc_start: 0.7899 (mttp) cc_final: 0.7592 (mttp) REVERT: S 127 SER cc_start: 0.8422 (t) cc_final: 0.8067 (t) REVERT: T 24 THR cc_start: 0.7814 (m) cc_final: 0.7596 (p) REVERT: T 99 LYS cc_start: 0.8051 (ttpp) cc_final: 0.7622 (ttmm) REVERT: T 105 LEU cc_start: 0.8102 (tp) cc_final: 0.7791 (tp) REVERT: T 122 MET cc_start: 0.7404 (tpt) cc_final: 0.7157 (mmm) REVERT: T 123 GLU cc_start: 0.7317 (mt-10) cc_final: 0.7003 (mt-10) REVERT: T 134 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8113 (mtmm) REVERT: T 195 SER cc_start: 0.7915 (m) cc_final: 0.7662 (t) REVERT: T 295 TYR cc_start: 0.7699 (m-80) cc_final: 0.7454 (m-80) REVERT: T 317 ASP cc_start: 0.7377 (t0) cc_final: 0.7060 (t0) REVERT: T 331 ASN cc_start: 0.7996 (m-40) cc_final: 0.7631 (m110) REVERT: T 362 ASP cc_start: 0.7864 (t0) cc_final: 0.7658 (m-30) REVERT: T 365 ASP cc_start: 0.7761 (m-30) cc_final: 0.7374 (m-30) REVERT: T 385 GLU cc_start: 0.7706 (tt0) cc_final: 0.7328 (tm-30) REVERT: T 392 ARG cc_start: 0.7473 (mtm110) cc_final: 0.7146 (mtm110) REVERT: T 401 ASP cc_start: 0.7720 (m-30) cc_final: 0.7440 (p0) REVERT: T 417 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7154 (mt0) REVERT: T 441 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7225 (tp30) REVERT: U 65 THR cc_start: 0.7447 (p) cc_final: 0.7131 (t) REVERT: U 105 GLU cc_start: 0.7955 (tt0) cc_final: 0.7692 (tt0) REVERT: U 107 PHE cc_start: 0.8581 (m-80) cc_final: 0.8111 (m-80) REVERT: U 110 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7199 (pp20) REVERT: U 131 GLU cc_start: 0.6986 (pt0) cc_final: 0.6681 (pt0) REVERT: U 142 GLU cc_start: 0.6611 (tm-30) cc_final: 0.5714 (tm-30) REVERT: U 144 GLN cc_start: 0.6603 (OUTLIER) cc_final: 0.5556 (mp10) REVERT: U 157 LYS cc_start: 0.7698 (mttt) cc_final: 0.6939 (mttm) REVERT: U 185 LEU cc_start: 0.8054 (mp) cc_final: 0.7724 (mp) REVERT: U 188 ASP cc_start: 0.8033 (m-30) cc_final: 0.7505 (m-30) REVERT: U 193 ASP cc_start: 0.7750 (t0) cc_final: 0.7099 (t0) REVERT: U 228 GLU cc_start: 0.7667 (mm-30) cc_final: 0.6853 (mm-30) REVERT: U 233 LYS cc_start: 0.7309 (mmmt) cc_final: 0.6887 (mmmt) REVERT: U 264 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7433 (mm-30) REVERT: U 281 LYS cc_start: 0.7980 (ttmm) cc_final: 0.7636 (tttp) REVERT: U 282 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7163 (mt-10) REVERT: U 283 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6793 (mt-10) REVERT: U 339 SER cc_start: 0.8362 (m) cc_final: 0.8140 (t) REVERT: U 374 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7374 (mm-30) REVERT: U 413 ARG cc_start: 0.7409 (mtm110) cc_final: 0.6952 (ptm-80) REVERT: U 451 GLN cc_start: 0.7353 (mm-40) cc_final: 0.7083 (mp10) REVERT: V 42 LYS cc_start: 0.7273 (mtmm) cc_final: 0.6318 (tttm) REVERT: V 99 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7758 (mtpt) REVERT: V 109 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7724 (mt-10) REVERT: V 135 GLU cc_start: 0.7435 (tt0) cc_final: 0.7122 (tt0) REVERT: V 144 VAL cc_start: 0.7652 (t) cc_final: 0.7221 (m) REVERT: V 165 HIS cc_start: 0.7459 (m170) cc_final: 0.7212 (m-70) REVERT: V 177 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7594 (ttpp) REVERT: V 178 THR cc_start: 0.7997 (m) cc_final: 0.7637 (p) REVERT: V 180 ARG cc_start: 0.7798 (ttp-170) cc_final: 0.7569 (ttp80) REVERT: V 182 ASP cc_start: 0.7379 (p0) cc_final: 0.7172 (p0) REVERT: V 193 LYS cc_start: 0.7795 (mtpt) cc_final: 0.7527 (mtpt) REVERT: V 198 ASP cc_start: 0.7135 (m-30) cc_final: 0.6840 (m-30) REVERT: V 214 ARG cc_start: 0.7289 (mmt180) cc_final: 0.6588 (mmm-85) REVERT: V 227 GLU cc_start: 0.7568 (tt0) cc_final: 0.7157 (mm-30) REVERT: V 294 LYS cc_start: 0.7545 (tppt) cc_final: 0.7318 (tppt) REVERT: V 297 ASP cc_start: 0.7810 (t0) cc_final: 0.7477 (t0) REVERT: V 302 GLU cc_start: 0.7176 (pt0) cc_final: 0.6842 (pt0) REVERT: V 326 LYS cc_start: 0.7454 (tmmt) cc_final: 0.7089 (tppt) REVERT: V 355 SER cc_start: 0.8098 (m) cc_final: 0.7609 (t) REVERT: V 394 GLN cc_start: 0.7685 (mt0) cc_final: 0.7318 (pt0) REVERT: V 454 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7808 (ttmm) REVERT: W 38 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7111 (mtt90) REVERT: W 146 ASP cc_start: 0.8595 (m-30) cc_final: 0.8314 (m-30) REVERT: W 167 THR cc_start: 0.7975 (p) cc_final: 0.7723 (t) REVERT: W 170 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7501 (mp0) REVERT: W 181 LYS cc_start: 0.7493 (ttpp) cc_final: 0.7157 (ttpp) REVERT: W 182 GLU cc_start: 0.7883 (tt0) cc_final: 0.7496 (tm-30) REVERT: W 189 VAL cc_start: 0.7272 (p) cc_final: 0.7009 (m) REVERT: W 193 ASP cc_start: 0.7502 (t0) cc_final: 0.7190 (t0) REVERT: W 204 ARG cc_start: 0.7058 (ttt90) cc_final: 0.6640 (ttt90) REVERT: W 266 ARG cc_start: 0.7153 (mtm-85) cc_final: 0.6562 (mtm-85) REVERT: W 302 ASP cc_start: 0.7139 (t0) cc_final: 0.6647 (t0) REVERT: W 304 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6726 (mp0) REVERT: W 331 LYS cc_start: 0.8506 (tttp) cc_final: 0.8245 (mtpp) REVERT: W 338 LYS cc_start: 0.8109 (mtpt) cc_final: 0.7815 (mttm) REVERT: W 376 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: W 378 GLU cc_start: 0.7913 (mp0) cc_final: 0.7090 (tm-30) REVERT: W 388 THR cc_start: 0.8239 (m) cc_final: 0.7972 (p) REVERT: W 393 GLU cc_start: 0.7930 (tt0) cc_final: 0.7598 (mt-10) REVERT: W 413 ARG cc_start: 0.7685 (mtp180) cc_final: 0.7233 (mtm180) REVERT: W 438 LYS cc_start: 0.7941 (tppp) cc_final: 0.7585 (tppp) REVERT: W 443 ASN cc_start: 0.6828 (m110) cc_final: 0.6537 (m-40) REVERT: W 451 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7540 (mm110) REVERT: X 77 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6353 (pp) REVERT: X 132 ARG cc_start: 0.7894 (tpp80) cc_final: 0.7372 (ttm-80) REVERT: X 138 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7128 (tm-30) REVERT: X 171 LYS cc_start: 0.7943 (tttt) cc_final: 0.7652 (tppt) REVERT: X 210 LYS cc_start: 0.7358 (ptmt) cc_final: 0.7035 (ptmt) REVERT: X 211 ARG cc_start: 0.7722 (mtp-110) cc_final: 0.7185 (mtp180) REVERT: X 228 GLU cc_start: 0.6756 (pt0) cc_final: 0.6277 (pt0) REVERT: X 240 LYS cc_start: 0.8341 (mtmt) cc_final: 0.8044 (mmmm) REVERT: X 242 GLU cc_start: 0.7522 (mp0) cc_final: 0.7316 (mp0) REVERT: X 276 LYS cc_start: 0.7511 (tttm) cc_final: 0.7072 (tmtt) REVERT: X 282 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6297 (tp30) REVERT: X 290 LYS cc_start: 0.7654 (ttmm) cc_final: 0.7273 (mtmt) REVERT: X 315 MET cc_start: 0.7883 (mmp) cc_final: 0.7573 (mmm) REVERT: X 317 ASP cc_start: 0.6686 (OUTLIER) cc_final: 0.6362 (p0) REVERT: X 432 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8257 (mmmm) REVERT: X 434 ILE cc_start: 0.7185 (mt) cc_final: 0.6848 (tt) REVERT: X 438 ASP cc_start: 0.7884 (m-30) cc_final: 0.7650 (m-30) REVERT: Y 132 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: Y 144 GLN cc_start: 0.6709 (tt0) cc_final: 0.6216 (tt0) REVERT: Y 160 ILE cc_start: 0.7915 (tt) cc_final: 0.7615 (tp) REVERT: Y 170 GLU cc_start: 0.6455 (mp0) cc_final: 0.6150 (mt-10) REVERT: Y 210 ARG cc_start: 0.8090 (mmm160) cc_final: 0.7629 (mmm160) REVERT: Y 215 MET cc_start: 0.7003 (mtp) cc_final: 0.6798 (mtp) REVERT: Y 228 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7453 (mm-30) REVERT: Y 283 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6843 (mt-10) REVERT: Y 317 PHE cc_start: 0.8550 (m-80) cc_final: 0.8303 (m-80) REVERT: Y 361 GLU cc_start: 0.7225 (tt0) cc_final: 0.6965 (tp30) REVERT: Y 378 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6768 (mm-30) REVERT: Y 392 VAL cc_start: 0.7694 (t) cc_final: 0.7399 (p) REVERT: Y 415 ASN cc_start: 0.7346 (t0) cc_final: 0.6842 (t0) REVERT: Y 443 ASN cc_start: 0.7464 (m110) cc_final: 0.7064 (m110) REVERT: Y 444 GLU cc_start: 0.7543 (tt0) cc_final: 0.7067 (tp30) REVERT: Y 449 ASP cc_start: 0.7540 (t70) cc_final: 0.6987 (m-30) REVERT: Y 453 ASN cc_start: 0.7890 (m110) cc_final: 0.7566 (m-40) REVERT: Z 311 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7460 (mtp85) outliers start: 129 outliers final: 81 residues processed: 991 average time/residue: 0.4682 time to fit residues: 705.5841 Evaluate side-chains 1004 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 912 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1103 ASP Chi-restraints excluded: chain Q residue 1134 GLU Chi-restraints excluded: chain Q residue 1150 LYS Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1301 LEU Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain R residue 750 THR Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 417 GLN Chi-restraints excluded: chain T residue 438 ASP Chi-restraints excluded: chain T residue 448 ASP Chi-restraints excluded: chain U residue 32 ASP Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain U residue 235 VAL Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 316 GLU Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 243 ILE Chi-restraints excluded: chain V residue 278 THR Chi-restraints excluded: chain V residue 314 ASN Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain W residue 429 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 182 ASP Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 132 GLU Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 418 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 1.9990 chunk 314 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 204 optimal weight: 0.2980 chunk 86 optimal weight: 0.0470 chunk 349 optimal weight: 0.6980 chunk 289 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 183 optimal weight: 0.0170 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS R 666 ASN ** R 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 256 ASN T 417 GLN V 325 ASN W 360 ASN X 256 ASN X 289 ASN X 325 ASN Y 230 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 29102 Z= 0.159 Angle : 0.536 8.699 39373 Z= 0.262 Chirality : 0.042 0.192 4620 Planarity : 0.003 0.033 5040 Dihedral : 6.416 136.390 4004 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.73 % Allowed : 25.66 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3618 helix: 0.94 (0.14), residues: 1471 sheet: 0.64 (0.19), residues: 675 loop : -0.82 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q1361 HIS 0.008 0.001 HIS V 165 PHE 0.024 0.001 PHE R 70 TYR 0.018 0.001 TYR U 427 ARG 0.008 0.000 ARG Y 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 914 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1112 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7906 (mtpp) REVERT: Q 1134 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7560 (mm-30) REVERT: Q 1139 GLU cc_start: 0.7208 (tp30) cc_final: 0.6026 (tp30) REVERT: Q 1142 ARG cc_start: 0.7150 (ttp-110) cc_final: 0.6850 (ptp90) REVERT: Q 1189 SER cc_start: 0.7897 (t) cc_final: 0.7480 (p) REVERT: Q 1208 ARG cc_start: 0.7879 (ttm170) cc_final: 0.7444 (tpp80) REVERT: Q 1255 TYR cc_start: 0.7689 (t80) cc_final: 0.7240 (t80) REVERT: Q 1287 SER cc_start: 0.8012 (m) cc_final: 0.7655 (t) REVERT: Q 1316 HIS cc_start: 0.7687 (m-70) cc_final: 0.6864 (m-70) REVERT: Q 1327 MET cc_start: 0.6020 (mmm) cc_final: 0.5710 (mmm) REVERT: Q 1331 MET cc_start: 0.7486 (mmm) cc_final: 0.7265 (mmm) REVERT: Q 1432 MET cc_start: 0.4635 (tpp) cc_final: 0.4069 (tpp) REVERT: R 65 ASN cc_start: 0.8276 (t0) cc_final: 0.8011 (t0) REVERT: R 79 PHE cc_start: 0.8067 (m-10) cc_final: 0.7774 (m-10) REVERT: R 85 ASP cc_start: 0.8802 (m-30) cc_final: 0.8542 (m-30) REVERT: R 93 ARG cc_start: 0.8543 (tmm-80) cc_final: 0.8095 (ttp-170) REVERT: R 95 GLN cc_start: 0.8917 (mt0) cc_final: 0.8601 (mt0) REVERT: R 97 ARG cc_start: 0.7903 (ttp-110) cc_final: 0.7657 (ttp-110) REVERT: R 144 GLN cc_start: 0.6807 (pt0) cc_final: 0.6516 (pt0) REVERT: R 192 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7298 (mm-30) REVERT: R 242 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7405 (mt0) REVERT: R 244 GLU cc_start: 0.7726 (tt0) cc_final: 0.7423 (tt0) REVERT: R 249 ASP cc_start: 0.8130 (m-30) cc_final: 0.7860 (m-30) REVERT: R 260 ASP cc_start: 0.7401 (m-30) cc_final: 0.6981 (m-30) REVERT: R 262 GLU cc_start: 0.7780 (mp0) cc_final: 0.7116 (mp0) REVERT: R 264 ILE cc_start: 0.8172 (tt) cc_final: 0.7741 (tp) REVERT: R 269 ASN cc_start: 0.7177 (t0) cc_final: 0.6600 (t0) REVERT: R 270 LEU cc_start: 0.8372 (mt) cc_final: 0.8122 (mm) REVERT: R 601 HIS cc_start: 0.7666 (t70) cc_final: 0.7022 (t-170) REVERT: R 608 GLU cc_start: 0.7655 (mt-10) cc_final: 0.6944 (tt0) REVERT: R 677 VAL cc_start: 0.8652 (t) cc_final: 0.8359 (m) REVERT: R 709 ASP cc_start: 0.7482 (m-30) cc_final: 0.7220 (m-30) REVERT: R 720 ASN cc_start: 0.7528 (t0) cc_final: 0.6618 (t0) REVERT: R 723 GLN cc_start: 0.7613 (mp10) cc_final: 0.6584 (mp10) REVERT: R 724 TYR cc_start: 0.7720 (t80) cc_final: 0.7276 (t80) REVERT: R 726 LYS cc_start: 0.8309 (mptt) cc_final: 0.8097 (mtmm) REVERT: R 736 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7197 (tm-30) REVERT: S 114 LYS cc_start: 0.7897 (mttp) cc_final: 0.7616 (mttp) REVERT: S 127 SER cc_start: 0.8410 (t) cc_final: 0.8043 (t) REVERT: T 99 LYS cc_start: 0.8032 (ttpp) cc_final: 0.7611 (ttmm) REVERT: T 105 LEU cc_start: 0.8087 (tp) cc_final: 0.7801 (tp) REVERT: T 122 MET cc_start: 0.7408 (tpt) cc_final: 0.7158 (mmm) REVERT: T 123 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6993 (mt-10) REVERT: T 134 LYS cc_start: 0.8460 (mtpp) cc_final: 0.8106 (mtmm) REVERT: T 195 SER cc_start: 0.7929 (m) cc_final: 0.7675 (t) REVERT: T 295 TYR cc_start: 0.7686 (m-80) cc_final: 0.7464 (m-80) REVERT: T 317 ASP cc_start: 0.7385 (t0) cc_final: 0.7071 (t0) REVERT: T 331 ASN cc_start: 0.7998 (m-40) cc_final: 0.7635 (m110) REVERT: T 362 ASP cc_start: 0.7869 (t0) cc_final: 0.7641 (m-30) REVERT: T 365 ASP cc_start: 0.7743 (m-30) cc_final: 0.7356 (m-30) REVERT: T 385 GLU cc_start: 0.7725 (tt0) cc_final: 0.7331 (tm-30) REVERT: T 392 ARG cc_start: 0.7474 (mtm110) cc_final: 0.7145 (mtm110) REVERT: T 417 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7089 (mt0) REVERT: T 430 ASN cc_start: 0.8282 (p0) cc_final: 0.8058 (p0) REVERT: T 441 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7228 (tp30) REVERT: U 65 THR cc_start: 0.7430 (p) cc_final: 0.7126 (t) REVERT: U 105 GLU cc_start: 0.7945 (tt0) cc_final: 0.7678 (tt0) REVERT: U 107 PHE cc_start: 0.8557 (m-80) cc_final: 0.8095 (m-80) REVERT: U 110 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7205 (pp20) REVERT: U 142 GLU cc_start: 0.6587 (tm-30) cc_final: 0.5697 (tm-30) REVERT: U 144 GLN cc_start: 0.6559 (OUTLIER) cc_final: 0.5546 (mp10) REVERT: U 157 LYS cc_start: 0.7668 (mttt) cc_final: 0.6934 (mttm) REVERT: U 185 LEU cc_start: 0.8065 (mp) cc_final: 0.7710 (mp) REVERT: U 188 ASP cc_start: 0.7988 (m-30) cc_final: 0.7462 (m-30) REVERT: U 193 ASP cc_start: 0.7702 (t0) cc_final: 0.7029 (t0) REVERT: U 228 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6817 (mm-30) REVERT: U 233 LYS cc_start: 0.7307 (mmmt) cc_final: 0.6884 (mmmt) REVERT: U 264 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7435 (mm-30) REVERT: U 281 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7622 (tttp) REVERT: U 282 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7159 (mt-10) REVERT: U 283 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6752 (mt-10) REVERT: U 339 SER cc_start: 0.8378 (m) cc_final: 0.8139 (t) REVERT: U 374 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7381 (mm-30) REVERT: U 413 ARG cc_start: 0.7397 (mtm110) cc_final: 0.6847 (ptm-80) REVERT: U 451 GLN cc_start: 0.7382 (mm-40) cc_final: 0.7071 (mp10) REVERT: V 42 LYS cc_start: 0.7256 (mtmm) cc_final: 0.6312 (tttm) REVERT: V 99 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7763 (mtpt) REVERT: V 109 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7657 (mt-10) REVERT: V 135 GLU cc_start: 0.7428 (tt0) cc_final: 0.7137 (tt0) REVERT: V 144 VAL cc_start: 0.7642 (t) cc_final: 0.7216 (m) REVERT: V 161 LYS cc_start: 0.8265 (mttp) cc_final: 0.7932 (mttp) REVERT: V 178 THR cc_start: 0.7979 (m) cc_final: 0.7705 (p) REVERT: V 193 LYS cc_start: 0.7789 (mtpt) cc_final: 0.7525 (mtpt) REVERT: V 198 ASP cc_start: 0.7142 (m-30) cc_final: 0.6835 (m-30) REVERT: V 214 ARG cc_start: 0.7296 (mmt180) cc_final: 0.6603 (mmm-85) REVERT: V 227 GLU cc_start: 0.7573 (tt0) cc_final: 0.7116 (mm-30) REVERT: V 294 LYS cc_start: 0.7543 (tppt) cc_final: 0.7314 (tppt) REVERT: V 297 ASP cc_start: 0.7830 (t0) cc_final: 0.7505 (t0) REVERT: V 302 GLU cc_start: 0.7135 (pt0) cc_final: 0.6787 (pt0) REVERT: V 326 LYS cc_start: 0.7446 (tmmt) cc_final: 0.7080 (tppt) REVERT: V 355 SER cc_start: 0.8058 (m) cc_final: 0.7581 (t) REVERT: V 385 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7116 (mm-30) REVERT: V 394 GLN cc_start: 0.7678 (mt0) cc_final: 0.7316 (pt0) REVERT: V 454 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7802 (ttmm) REVERT: W 38 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7292 (mtt90) REVERT: W 146 ASP cc_start: 0.8575 (m-30) cc_final: 0.8337 (m-30) REVERT: W 147 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.7187 (mtm-85) REVERT: W 167 THR cc_start: 0.7973 (p) cc_final: 0.7720 (t) REVERT: W 170 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7518 (mp0) REVERT: W 181 LYS cc_start: 0.7462 (ttpp) cc_final: 0.7064 (ttpp) REVERT: W 182 GLU cc_start: 0.7868 (tt0) cc_final: 0.7382 (tm-30) REVERT: W 189 VAL cc_start: 0.7277 (p) cc_final: 0.7028 (m) REVERT: W 193 ASP cc_start: 0.7447 (t0) cc_final: 0.7082 (t0) REVERT: W 204 ARG cc_start: 0.6989 (ttt90) cc_final: 0.6583 (ttt90) REVERT: W 266 ARG cc_start: 0.7147 (mtm-85) cc_final: 0.6535 (mtm-85) REVERT: W 302 ASP cc_start: 0.6970 (t0) cc_final: 0.6489 (t0) REVERT: W 304 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6810 (mp0) REVERT: W 327 ARG cc_start: 0.8218 (ttm170) cc_final: 0.7902 (ttm-80) REVERT: W 331 LYS cc_start: 0.8503 (tttp) cc_final: 0.8215 (mtpp) REVERT: W 338 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7819 (mttm) REVERT: W 376 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: W 378 GLU cc_start: 0.7922 (mp0) cc_final: 0.7157 (tm-30) REVERT: W 388 THR cc_start: 0.8233 (m) cc_final: 0.7976 (p) REVERT: W 393 GLU cc_start: 0.7926 (tt0) cc_final: 0.7615 (mt-10) REVERT: W 413 ARG cc_start: 0.7687 (mtp180) cc_final: 0.7229 (mtm180) REVERT: W 438 LYS cc_start: 0.7940 (tppp) cc_final: 0.7563 (tppp) REVERT: W 443 ASN cc_start: 0.6771 (m110) cc_final: 0.6477 (m-40) REVERT: X 77 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6467 (pp) REVERT: X 109 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6479 (mt-10) REVERT: X 132 ARG cc_start: 0.7861 (tpp80) cc_final: 0.7345 (ttm-80) REVERT: X 138 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7169 (tm-30) REVERT: X 144 VAL cc_start: 0.8336 (t) cc_final: 0.8135 (p) REVERT: X 171 LYS cc_start: 0.7942 (tttt) cc_final: 0.7688 (tppt) REVERT: X 187 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7117 (tm-30) REVERT: X 210 LYS cc_start: 0.7349 (ptmt) cc_final: 0.6983 (ptmt) REVERT: X 211 ARG cc_start: 0.7719 (mtp-110) cc_final: 0.7399 (mtp180) REVERT: X 228 GLU cc_start: 0.6789 (pt0) cc_final: 0.6344 (pt0) REVERT: X 240 LYS cc_start: 0.8321 (mtmt) cc_final: 0.8026 (mmmm) REVERT: X 276 LYS cc_start: 0.7484 (tttm) cc_final: 0.7090 (tmtt) REVERT: X 282 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6668 (tp30) REVERT: X 290 LYS cc_start: 0.7652 (ttmm) cc_final: 0.7271 (mtmt) REVERT: X 315 MET cc_start: 0.7863 (mmp) cc_final: 0.7546 (mmm) REVERT: X 317 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.6332 (p0) REVERT: X 371 ARG cc_start: 0.8506 (ttp-170) cc_final: 0.8252 (ttp80) REVERT: X 432 LYS cc_start: 0.8517 (mmmt) cc_final: 0.8233 (mmmm) REVERT: X 434 ILE cc_start: 0.7197 (mt) cc_final: 0.6853 (tt) REVERT: X 438 ASP cc_start: 0.7875 (m-30) cc_final: 0.7651 (m-30) REVERT: Y 132 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7890 (mp0) REVERT: Y 144 GLN cc_start: 0.6701 (tt0) cc_final: 0.6202 (tt0) REVERT: Y 160 ILE cc_start: 0.7885 (tt) cc_final: 0.7594 (tp) REVERT: Y 170 GLU cc_start: 0.6468 (mp0) cc_final: 0.6150 (mt-10) REVERT: Y 210 ARG cc_start: 0.8115 (mmm160) cc_final: 0.7644 (mmm160) REVERT: Y 215 MET cc_start: 0.6887 (mtp) cc_final: 0.6665 (mtp) REVERT: Y 228 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7469 (mm-30) REVERT: Y 297 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7374 (mt-10) REVERT: Y 317 PHE cc_start: 0.8528 (m-80) cc_final: 0.8272 (m-80) REVERT: Y 361 GLU cc_start: 0.7204 (tt0) cc_final: 0.6912 (tp30) REVERT: Y 373 GLN cc_start: 0.7807 (tt0) cc_final: 0.7403 (mt0) REVERT: Y 378 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6606 (mm-30) REVERT: Y 415 ASN cc_start: 0.7327 (t0) cc_final: 0.6751 (t0) REVERT: Y 417 THR cc_start: 0.7594 (p) cc_final: 0.7106 (t) REVERT: Y 443 ASN cc_start: 0.7483 (m110) cc_final: 0.7071 (m110) REVERT: Y 444 GLU cc_start: 0.7529 (tt0) cc_final: 0.7069 (tp30) REVERT: Y 449 ASP cc_start: 0.7543 (t70) cc_final: 0.7004 (m-30) REVERT: Y 453 ASN cc_start: 0.7871 (m110) cc_final: 0.7561 (m-40) REVERT: Z 311 ARG cc_start: 0.7944 (ttm110) cc_final: 0.7601 (mtp85) outliers start: 118 outliers final: 80 residues processed: 974 average time/residue: 0.4690 time to fit residues: 693.0600 Evaluate side-chains 992 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 902 time to evaluate : 3.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1134 GLU Chi-restraints excluded: chain Q residue 1150 LYS Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1243 SER Chi-restraints excluded: chain Q residue 1267 ASP Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1301 LEU Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain R residue 750 THR Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 246 ASP Chi-restraints excluded: chain T residue 314 ASN Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 417 GLN Chi-restraints excluded: chain T residue 438 ASP Chi-restraints excluded: chain T residue 448 ASP Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 32 ASP Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 316 GLU Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 243 ILE Chi-restraints excluded: chain V residue 278 THR Chi-restraints excluded: chain V residue 314 ASN Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain W residue 429 LEU Chi-restraints excluded: chain W residue 444 GLU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 109 GLU Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 418 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 199 optimal weight: 0.3980 chunk 255 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 294 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 347 optimal weight: 0.9980 chunk 217 optimal weight: 0.0670 chunk 212 optimal weight: 2.9990 chunk 160 optimal weight: 0.4980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS ** R 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 666 ASN ** R 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 256 ASN T 417 GLN T 440 ASN V 165 HIS W 360 ASN X 289 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29102 Z= 0.181 Angle : 0.541 7.590 39373 Z= 0.263 Chirality : 0.042 0.200 4620 Planarity : 0.003 0.034 5040 Dihedral : 6.333 135.664 4004 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.64 % Allowed : 25.72 % Favored : 70.64 % 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: 0.30 (0.14), residues: 3618 helix: 1.00 (0.14), residues: 1472 sheet: 0.64 (0.20), residues: 665 loop : -0.77 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q1361 HIS 0.017 0.001 HIS R 121 PHE 0.017 0.001 PHE R 691 TYR 0.018 0.001 TYR U 427 ARG 0.008 0.000 ARG V 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 919 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7078 (p0) REVERT: Q 1112 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7891 (mtpp) REVERT: Q 1134 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: Q 1139 GLU cc_start: 0.7242 (tp30) cc_final: 0.6045 (tp30) REVERT: Q 1142 ARG cc_start: 0.7140 (ttp-110) cc_final: 0.6829 (ptp90) REVERT: Q 1189 SER cc_start: 0.7896 (t) cc_final: 0.7486 (p) REVERT: Q 1208 ARG cc_start: 0.7891 (ttm170) cc_final: 0.7472 (tpp80) REVERT: Q 1255 TYR cc_start: 0.7707 (t80) cc_final: 0.7255 (t80) REVERT: Q 1287 SER cc_start: 0.8008 (m) cc_final: 0.7650 (t) REVERT: Q 1316 HIS cc_start: 0.7691 (m-70) cc_final: 0.6843 (m-70) REVERT: Q 1327 MET cc_start: 0.6083 (mmm) cc_final: 0.5858 (mmm) REVERT: Q 1331 MET cc_start: 0.7479 (mmm) cc_final: 0.7256 (mmm) REVERT: Q 1432 MET cc_start: 0.4661 (tpp) cc_final: 0.4077 (tpp) REVERT: R 65 ASN cc_start: 0.8304 (t0) cc_final: 0.8051 (t0) REVERT: R 79 PHE cc_start: 0.8086 (m-10) cc_final: 0.7782 (m-10) REVERT: R 85 ASP cc_start: 0.8786 (m-30) cc_final: 0.8524 (m-30) REVERT: R 93 ARG cc_start: 0.8558 (tmm-80) cc_final: 0.8100 (ttp-170) REVERT: R 95 GLN cc_start: 0.8928 (mt0) cc_final: 0.8604 (mt0) REVERT: R 97 ARG cc_start: 0.7900 (ttp-110) cc_final: 0.7658 (ttp-110) REVERT: R 122 LEU cc_start: 0.7783 (mt) cc_final: 0.7441 (mm) REVERT: R 144 GLN cc_start: 0.6812 (pt0) cc_final: 0.6549 (pt0) REVERT: R 192 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7310 (mm-30) REVERT: R 242 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: R 244 GLU cc_start: 0.7743 (tt0) cc_final: 0.7436 (tt0) REVERT: R 249 ASP cc_start: 0.8157 (m-30) cc_final: 0.7869 (m-30) REVERT: R 260 ASP cc_start: 0.7389 (m-30) cc_final: 0.6978 (m-30) REVERT: R 262 GLU cc_start: 0.7777 (mp0) cc_final: 0.7125 (mp0) REVERT: R 264 ILE cc_start: 0.8166 (tt) cc_final: 0.7749 (tp) REVERT: R 269 ASN cc_start: 0.7198 (t0) cc_final: 0.6601 (t0) REVERT: R 270 LEU cc_start: 0.8380 (mt) cc_final: 0.8121 (mm) REVERT: R 601 HIS cc_start: 0.7654 (t70) cc_final: 0.7012 (t-170) REVERT: R 608 GLU cc_start: 0.7634 (mt-10) cc_final: 0.6906 (tt0) REVERT: R 677 VAL cc_start: 0.8637 (t) cc_final: 0.8314 (m) REVERT: R 682 GLU cc_start: 0.8092 (mp0) cc_final: 0.7866 (mp0) REVERT: R 709 ASP cc_start: 0.7509 (m-30) cc_final: 0.7216 (m-30) REVERT: R 720 ASN cc_start: 0.7545 (t0) cc_final: 0.6584 (t0) REVERT: R 722 GLU cc_start: 0.7403 (mp0) cc_final: 0.7061 (mp0) REVERT: R 723 GLN cc_start: 0.7641 (mp10) cc_final: 0.6604 (mp10) REVERT: R 724 TYR cc_start: 0.7738 (t80) cc_final: 0.7298 (t80) REVERT: R 726 LYS cc_start: 0.8325 (mptt) cc_final: 0.8116 (mtmm) REVERT: R 736 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7155 (tm-30) REVERT: S 114 LYS cc_start: 0.7904 (mttp) cc_final: 0.7618 (mttp) REVERT: S 127 SER cc_start: 0.8418 (t) cc_final: 0.8045 (t) REVERT: T 99 LYS cc_start: 0.8042 (ttpp) cc_final: 0.7565 (ttmm) REVERT: T 105 LEU cc_start: 0.8063 (tp) cc_final: 0.7726 (tp) REVERT: T 122 MET cc_start: 0.7421 (tpt) cc_final: 0.7172 (mmm) REVERT: T 123 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6994 (mt-10) REVERT: T 134 LYS cc_start: 0.8457 (mtpp) cc_final: 0.8111 (mtmm) REVERT: T 195 SER cc_start: 0.7914 (m) cc_final: 0.7657 (t) REVERT: T 276 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7680 (pttt) REVERT: T 295 TYR cc_start: 0.7687 (m-80) cc_final: 0.7455 (m-80) REVERT: T 317 ASP cc_start: 0.7382 (t0) cc_final: 0.7042 (t0) REVERT: T 331 ASN cc_start: 0.8009 (m-40) cc_final: 0.7654 (m110) REVERT: T 362 ASP cc_start: 0.7863 (t0) cc_final: 0.7640 (m-30) REVERT: T 365 ASP cc_start: 0.7737 (m-30) cc_final: 0.7354 (m-30) REVERT: T 385 GLU cc_start: 0.7745 (tt0) cc_final: 0.7313 (tm-30) REVERT: T 392 ARG cc_start: 0.7470 (mtm110) cc_final: 0.7143 (mtm110) REVERT: T 401 ASP cc_start: 0.7740 (m-30) cc_final: 0.7475 (p0) REVERT: T 417 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7201 (mt0) REVERT: T 430 ASN cc_start: 0.8294 (p0) cc_final: 0.8076 (p0) REVERT: T 441 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7267 (tp30) REVERT: U 65 THR cc_start: 0.7406 (p) cc_final: 0.7141 (t) REVERT: U 105 GLU cc_start: 0.7972 (tt0) cc_final: 0.7709 (tt0) REVERT: U 107 PHE cc_start: 0.8560 (m-80) cc_final: 0.8091 (m-80) REVERT: U 110 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7199 (pp20) REVERT: U 131 GLU cc_start: 0.7186 (pt0) cc_final: 0.6779 (pt0) REVERT: U 142 GLU cc_start: 0.6596 (tm-30) cc_final: 0.5731 (tm-30) REVERT: U 144 GLN cc_start: 0.6527 (OUTLIER) cc_final: 0.5526 (mp10) REVERT: U 157 LYS cc_start: 0.7680 (mttt) cc_final: 0.6947 (mttm) REVERT: U 185 LEU cc_start: 0.8050 (mp) cc_final: 0.7692 (mp) REVERT: U 188 ASP cc_start: 0.7968 (m-30) cc_final: 0.7446 (m-30) REVERT: U 193 ASP cc_start: 0.7691 (t0) cc_final: 0.7014 (t0) REVERT: U 228 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6791 (mm-30) REVERT: U 233 LYS cc_start: 0.7300 (mmmt) cc_final: 0.6929 (mmmt) REVERT: U 264 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7437 (mm-30) REVERT: U 281 LYS cc_start: 0.7985 (ttmm) cc_final: 0.7660 (tttp) REVERT: U 282 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7152 (mt-10) REVERT: U 283 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6737 (mt-10) REVERT: U 339 SER cc_start: 0.8386 (m) cc_final: 0.8131 (t) REVERT: U 374 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7376 (mm-30) REVERT: U 451 GLN cc_start: 0.7355 (mm-40) cc_final: 0.7051 (mp10) REVERT: V 42 LYS cc_start: 0.7210 (mtmm) cc_final: 0.6294 (tttm) REVERT: V 99 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7759 (mtpt) REVERT: V 109 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7643 (mt-10) REVERT: V 135 GLU cc_start: 0.7444 (tt0) cc_final: 0.7129 (tt0) REVERT: V 144 VAL cc_start: 0.7635 (t) cc_final: 0.7215 (m) REVERT: V 161 LYS cc_start: 0.8243 (mttp) cc_final: 0.7868 (mttp) REVERT: V 178 THR cc_start: 0.7965 (m) cc_final: 0.7678 (p) REVERT: V 180 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7654 (ttp80) REVERT: V 193 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7553 (mtpt) REVERT: V 198 ASP cc_start: 0.7154 (m-30) cc_final: 0.6845 (m-30) REVERT: V 214 ARG cc_start: 0.7300 (mmt180) cc_final: 0.6605 (mmm-85) REVERT: V 227 GLU cc_start: 0.7571 (tt0) cc_final: 0.7146 (mm-30) REVERT: V 294 LYS cc_start: 0.7540 (tppt) cc_final: 0.7318 (tppt) REVERT: V 297 ASP cc_start: 0.7836 (t0) cc_final: 0.7516 (t0) REVERT: V 302 GLU cc_start: 0.7147 (pt0) cc_final: 0.6770 (pt0) REVERT: V 326 LYS cc_start: 0.7451 (tmmt) cc_final: 0.7096 (tppt) REVERT: V 355 SER cc_start: 0.8062 (m) cc_final: 0.7588 (t) REVERT: V 385 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7116 (mm-30) REVERT: V 394 GLN cc_start: 0.7656 (mt0) cc_final: 0.7265 (pt0) REVERT: V 454 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7811 (ttmm) REVERT: W 38 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7278 (mtt90) REVERT: W 146 ASP cc_start: 0.8590 (m-30) cc_final: 0.8340 (m-30) REVERT: W 167 THR cc_start: 0.7977 (p) cc_final: 0.7722 (t) REVERT: W 170 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7526 (mp0) REVERT: W 181 LYS cc_start: 0.7432 (ttpp) cc_final: 0.7157 (ttpp) REVERT: W 182 GLU cc_start: 0.7926 (tt0) cc_final: 0.7452 (tm-30) REVERT: W 193 ASP cc_start: 0.7469 (t0) cc_final: 0.7126 (t0) REVERT: W 204 ARG cc_start: 0.6984 (ttt90) cc_final: 0.6575 (ttt90) REVERT: W 266 ARG cc_start: 0.7143 (mtm-85) cc_final: 0.6538 (mtm-85) REVERT: W 302 ASP cc_start: 0.6970 (t0) cc_final: 0.6511 (t0) REVERT: W 304 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6721 (mp0) REVERT: W 327 ARG cc_start: 0.8214 (ttm170) cc_final: 0.7907 (ttm-80) REVERT: W 331 LYS cc_start: 0.8487 (tttp) cc_final: 0.8189 (mtpp) REVERT: W 338 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7861 (mttp) REVERT: W 376 GLU cc_start: 0.7256 (mp0) cc_final: 0.6950 (mp0) REVERT: W 378 GLU cc_start: 0.7944 (mp0) cc_final: 0.7184 (tm-30) REVERT: W 393 GLU cc_start: 0.7924 (tt0) cc_final: 0.7621 (mt-10) REVERT: W 413 ARG cc_start: 0.7638 (mtp180) cc_final: 0.7209 (mtm180) REVERT: W 422 ASP cc_start: 0.7900 (m-30) cc_final: 0.7581 (m-30) REVERT: W 438 LYS cc_start: 0.7964 (tppp) cc_final: 0.7590 (tppp) REVERT: W 443 ASN cc_start: 0.6771 (m110) cc_final: 0.6470 (m-40) REVERT: X 77 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6470 (pp) REVERT: X 132 ARG cc_start: 0.7873 (tpp80) cc_final: 0.7335 (ttm-80) REVERT: X 138 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7176 (tm-30) REVERT: X 144 VAL cc_start: 0.8330 (t) cc_final: 0.8128 (p) REVERT: X 171 LYS cc_start: 0.7961 (tttt) cc_final: 0.7675 (tppt) REVERT: X 187 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7134 (tm-30) REVERT: X 210 LYS cc_start: 0.7321 (ptmt) cc_final: 0.6990 (ptmt) REVERT: X 228 GLU cc_start: 0.6726 (pt0) cc_final: 0.6281 (pt0) REVERT: X 240 LYS cc_start: 0.8302 (mtmt) cc_final: 0.8035 (mmmm) REVERT: X 282 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6685 (tp30) REVERT: X 290 LYS cc_start: 0.7653 (ttmm) cc_final: 0.7272 (mtmt) REVERT: X 315 MET cc_start: 0.7860 (mmp) cc_final: 0.7539 (mmm) REVERT: X 317 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6338 (p0) REVERT: X 385 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7472 (tt0) REVERT: X 432 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8240 (mmmm) REVERT: X 434 ILE cc_start: 0.7206 (mt) cc_final: 0.6950 (tt) REVERT: X 438 ASP cc_start: 0.7875 (m-30) cc_final: 0.7652 (m-30) REVERT: Y 132 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7896 (mp0) REVERT: Y 144 GLN cc_start: 0.6707 (tt0) cc_final: 0.6213 (tt0) REVERT: Y 160 ILE cc_start: 0.7887 (tt) cc_final: 0.7569 (tp) REVERT: Y 164 ASP cc_start: 0.7709 (m-30) cc_final: 0.7500 (m-30) REVERT: Y 169 TYR cc_start: 0.7615 (m-80) cc_final: 0.7057 (m-80) REVERT: Y 170 GLU cc_start: 0.6516 (mp0) cc_final: 0.6202 (mt-10) REVERT: Y 210 ARG cc_start: 0.8133 (mmm160) cc_final: 0.7662 (mmm160) REVERT: Y 228 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7462 (mm-30) REVERT: Y 297 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7360 (mt-10) REVERT: Y 317 PHE cc_start: 0.8526 (m-80) cc_final: 0.8269 (m-80) REVERT: Y 361 GLU cc_start: 0.7186 (tt0) cc_final: 0.6907 (tp30) REVERT: Y 373 GLN cc_start: 0.7811 (tt0) cc_final: 0.7422 (mt0) REVERT: Y 378 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6701 (mm-30) REVERT: Y 415 ASN cc_start: 0.7321 (t0) cc_final: 0.6755 (t0) REVERT: Y 417 THR cc_start: 0.7559 (p) cc_final: 0.7074 (t) REVERT: Y 443 ASN cc_start: 0.7508 (m110) cc_final: 0.7099 (m110) REVERT: Y 444 GLU cc_start: 0.7551 (tt0) cc_final: 0.7089 (tp30) REVERT: Y 449 ASP cc_start: 0.7556 (t70) cc_final: 0.7011 (m-30) REVERT: Y 453 ASN cc_start: 0.7865 (m110) cc_final: 0.7555 (m-40) REVERT: Z 311 ARG cc_start: 0.7951 (ttm110) cc_final: 0.7615 (mtp85) REVERT: Z 314 GLU cc_start: 0.7887 (pt0) cc_final: 0.7655 (pt0) outliers start: 115 outliers final: 83 residues processed: 980 average time/residue: 0.5023 time to fit residues: 757.4120 Evaluate side-chains 1004 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 911 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1103 ASP Chi-restraints excluded: chain Q residue 1134 GLU Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1267 ASP Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain R residue 750 THR Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 246 ASP Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 276 LYS Chi-restraints excluded: chain T residue 314 ASN Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 417 GLN Chi-restraints excluded: chain T residue 448 ASP Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 32 ASP Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 316 GLU Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 433 SER Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 243 ILE Chi-restraints excluded: chain V residue 278 THR Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 314 ASN Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 346 ASP Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain W residue 429 LEU Chi-restraints excluded: chain W residue 444 GLU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 182 ASP Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 418 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 0.0770 chunk 138 optimal weight: 0.2980 chunk 207 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 221 optimal weight: 0.6980 chunk 237 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 273 optimal weight: 0.0670 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 107 ASN R 121 HIS R 666 ASN ** R 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 256 ASN T 417 GLN T 440 ASN W 90 GLN W 360 ASN X 256 ASN X 289 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29102 Z= 0.166 Angle : 0.539 8.076 39373 Z= 0.262 Chirality : 0.042 0.271 4620 Planarity : 0.003 0.041 5040 Dihedral : 6.227 133.307 4004 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.64 % Allowed : 25.72 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3618 helix: 1.06 (0.14), residues: 1471 sheet: 0.62 (0.20), residues: 667 loop : -0.73 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q1361 HIS 0.009 0.001 HIS V 165 PHE 0.027 0.001 PHE R 70 TYR 0.021 0.001 TYR Q1337 ARG 0.009 0.000 ARG X 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 912 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7089 (p0) REVERT: Q 1112 LYS cc_start: 0.8233 (mtpp) cc_final: 0.7906 (mtpp) REVERT: Q 1134 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7540 (mm-30) REVERT: Q 1139 GLU cc_start: 0.7231 (tp30) cc_final: 0.6545 (tp30) REVERT: Q 1142 ARG cc_start: 0.7132 (ttp-110) cc_final: 0.6833 (ptp90) REVERT: Q 1189 SER cc_start: 0.7892 (t) cc_final: 0.7485 (p) REVERT: Q 1208 ARG cc_start: 0.7868 (ttm170) cc_final: 0.7462 (tpp80) REVERT: Q 1255 TYR cc_start: 0.7705 (t80) cc_final: 0.7258 (t80) REVERT: Q 1287 SER cc_start: 0.8002 (m) cc_final: 0.7642 (t) REVERT: Q 1316 HIS cc_start: 0.7704 (m-70) cc_final: 0.6827 (m-70) REVERT: Q 1327 MET cc_start: 0.6080 (mmm) cc_final: 0.5868 (mmm) REVERT: Q 1331 MET cc_start: 0.7474 (mmm) cc_final: 0.7256 (mmm) REVERT: R 65 ASN cc_start: 0.8296 (t0) cc_final: 0.8044 (t0) REVERT: R 79 PHE cc_start: 0.8093 (m-10) cc_final: 0.7788 (m-10) REVERT: R 85 ASP cc_start: 0.8793 (m-30) cc_final: 0.8537 (m-30) REVERT: R 93 ARG cc_start: 0.8551 (tmm-80) cc_final: 0.8086 (ttp-170) REVERT: R 95 GLN cc_start: 0.8926 (mt0) cc_final: 0.8612 (mt0) REVERT: R 97 ARG cc_start: 0.7903 (ttp-110) cc_final: 0.7659 (ttp-110) REVERT: R 144 GLN cc_start: 0.6797 (pt0) cc_final: 0.6531 (pt0) REVERT: R 146 GLN cc_start: 0.7783 (mm110) cc_final: 0.7481 (mm110) REVERT: R 192 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7321 (mm-30) REVERT: R 242 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7424 (mt0) REVERT: R 244 GLU cc_start: 0.7756 (tt0) cc_final: 0.7446 (tt0) REVERT: R 249 ASP cc_start: 0.8202 (m-30) cc_final: 0.7919 (m-30) REVERT: R 260 ASP cc_start: 0.7366 (m-30) cc_final: 0.6959 (m-30) REVERT: R 262 GLU cc_start: 0.7772 (mp0) cc_final: 0.7096 (mp0) REVERT: R 264 ILE cc_start: 0.8149 (tt) cc_final: 0.7738 (tp) REVERT: R 269 ASN cc_start: 0.7201 (t0) cc_final: 0.6592 (t0) REVERT: R 270 LEU cc_start: 0.8381 (mt) cc_final: 0.8127 (mm) REVERT: R 601 HIS cc_start: 0.7637 (t70) cc_final: 0.6954 (t-170) REVERT: R 608 GLU cc_start: 0.7609 (mt-10) cc_final: 0.6880 (tt0) REVERT: R 677 VAL cc_start: 0.8635 (t) cc_final: 0.8303 (m) REVERT: R 682 GLU cc_start: 0.8100 (mp0) cc_final: 0.7875 (mp0) REVERT: R 709 ASP cc_start: 0.7504 (m-30) cc_final: 0.7184 (m-30) REVERT: R 720 ASN cc_start: 0.7547 (t0) cc_final: 0.6608 (t0) REVERT: R 722 GLU cc_start: 0.7395 (mp0) cc_final: 0.6993 (mp0) REVERT: R 723 GLN cc_start: 0.7622 (mp10) cc_final: 0.6569 (mp10) REVERT: R 724 TYR cc_start: 0.7709 (t80) cc_final: 0.7262 (t80) REVERT: R 726 LYS cc_start: 0.8314 (mptt) cc_final: 0.8108 (mtmm) REVERT: R 736 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7114 (tm-30) REVERT: S 47 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7304 (ttm110) REVERT: S 114 LYS cc_start: 0.7902 (mttp) cc_final: 0.7619 (mttp) REVERT: S 127 SER cc_start: 0.8416 (t) cc_final: 0.8060 (t) REVERT: T 99 LYS cc_start: 0.7998 (ttpp) cc_final: 0.7565 (ttmm) REVERT: T 105 LEU cc_start: 0.8041 (tp) cc_final: 0.7750 (tp) REVERT: T 122 MET cc_start: 0.7422 (tpt) cc_final: 0.7171 (mmm) REVERT: T 123 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6983 (mt-10) REVERT: T 134 LYS cc_start: 0.8469 (mtpp) cc_final: 0.8130 (mtmm) REVERT: T 182 ASP cc_start: 0.6548 (OUTLIER) cc_final: 0.6275 (p0) REVERT: T 195 SER cc_start: 0.7920 (m) cc_final: 0.7673 (t) REVERT: T 317 ASP cc_start: 0.7333 (t0) cc_final: 0.7045 (t0) REVERT: T 331 ASN cc_start: 0.7996 (m-40) cc_final: 0.7640 (m110) REVERT: T 362 ASP cc_start: 0.7830 (t0) cc_final: 0.7619 (m-30) REVERT: T 365 ASP cc_start: 0.7717 (m-30) cc_final: 0.7340 (m-30) REVERT: T 385 GLU cc_start: 0.7740 (tt0) cc_final: 0.7309 (tm-30) REVERT: T 430 ASN cc_start: 0.8303 (p0) cc_final: 0.8073 (p0) REVERT: T 441 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7327 (tp30) REVERT: U 65 THR cc_start: 0.7408 (p) cc_final: 0.7151 (t) REVERT: U 105 GLU cc_start: 0.7991 (tt0) cc_final: 0.7742 (tt0) REVERT: U 107 PHE cc_start: 0.8556 (m-80) cc_final: 0.8094 (m-80) REVERT: U 110 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7213 (pp20) REVERT: U 131 GLU cc_start: 0.7205 (pt0) cc_final: 0.6804 (pt0) REVERT: U 142 GLU cc_start: 0.6614 (tm-30) cc_final: 0.5702 (tm-30) REVERT: U 144 GLN cc_start: 0.6534 (OUTLIER) cc_final: 0.5508 (mp10) REVERT: U 157 LYS cc_start: 0.7670 (mttt) cc_final: 0.6862 (mttm) REVERT: U 170 GLU cc_start: 0.7127 (tp30) cc_final: 0.6838 (tp30) REVERT: U 185 LEU cc_start: 0.8070 (mp) cc_final: 0.7695 (mp) REVERT: U 188 ASP cc_start: 0.7930 (m-30) cc_final: 0.7427 (m-30) REVERT: U 193 ASP cc_start: 0.7671 (t0) cc_final: 0.7002 (t0) REVERT: U 228 GLU cc_start: 0.7656 (mm-30) cc_final: 0.6814 (mm-30) REVERT: U 233 LYS cc_start: 0.7351 (mmmt) cc_final: 0.7007 (mmmt) REVERT: U 264 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7442 (mm-30) REVERT: U 281 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7633 (tttp) REVERT: U 282 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7157 (mt-10) REVERT: U 283 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6749 (mt-10) REVERT: U 339 SER cc_start: 0.8392 (m) cc_final: 0.8132 (t) REVERT: U 374 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7383 (mm-30) REVERT: U 413 ARG cc_start: 0.7328 (mtm110) cc_final: 0.6771 (ptm-80) REVERT: U 451 GLN cc_start: 0.7337 (mm-40) cc_final: 0.7039 (mp10) REVERT: V 42 LYS cc_start: 0.7166 (mtmm) cc_final: 0.6270 (tttm) REVERT: V 99 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7754 (mtpt) REVERT: V 109 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7640 (mt-10) REVERT: V 135 GLU cc_start: 0.7454 (tt0) cc_final: 0.7134 (tt0) REVERT: V 144 VAL cc_start: 0.7648 (t) cc_final: 0.7232 (m) REVERT: V 161 LYS cc_start: 0.8237 (mttp) cc_final: 0.7851 (mttp) REVERT: V 193 LYS cc_start: 0.7813 (mtpt) cc_final: 0.7546 (mtpt) REVERT: V 198 ASP cc_start: 0.7161 (m-30) cc_final: 0.6816 (m-30) REVERT: V 214 ARG cc_start: 0.7305 (mmt180) cc_final: 0.6575 (mmm-85) REVERT: V 294 LYS cc_start: 0.7542 (tppt) cc_final: 0.7322 (tppt) REVERT: V 297 ASP cc_start: 0.7836 (t0) cc_final: 0.7522 (t0) REVERT: V 302 GLU cc_start: 0.7149 (pt0) cc_final: 0.6797 (pt0) REVERT: V 326 LYS cc_start: 0.7443 (tmmt) cc_final: 0.7092 (tppt) REVERT: V 355 SER cc_start: 0.8034 (m) cc_final: 0.7569 (t) REVERT: V 385 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7153 (mm-30) REVERT: V 394 GLN cc_start: 0.7641 (mt0) cc_final: 0.7244 (pt0) REVERT: V 454 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7810 (ttmm) REVERT: W 38 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.7259 (mtt90) REVERT: W 146 ASP cc_start: 0.8592 (m-30) cc_final: 0.8363 (m-30) REVERT: W 167 THR cc_start: 0.7997 (p) cc_final: 0.7740 (t) REVERT: W 170 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7521 (mp0) REVERT: W 182 GLU cc_start: 0.7957 (tt0) cc_final: 0.7456 (tm-30) REVERT: W 193 ASP cc_start: 0.7482 (t0) cc_final: 0.7136 (t0) REVERT: W 204 ARG cc_start: 0.6968 (ttt90) cc_final: 0.6565 (ttt90) REVERT: W 266 ARG cc_start: 0.7140 (mtm-85) cc_final: 0.6518 (mtm-85) REVERT: W 302 ASP cc_start: 0.6951 (t0) cc_final: 0.6472 (t0) REVERT: W 304 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6809 (mp0) REVERT: W 327 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7909 (ttm-80) REVERT: W 331 LYS cc_start: 0.8469 (tttp) cc_final: 0.8166 (mtpp) REVERT: W 338 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7843 (mttp) REVERT: W 376 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: W 378 GLU cc_start: 0.7949 (mp0) cc_final: 0.7221 (tm-30) REVERT: W 393 GLU cc_start: 0.7915 (tt0) cc_final: 0.7589 (mt-10) REVERT: W 413 ARG cc_start: 0.7647 (mtp180) cc_final: 0.7234 (mtm180) REVERT: W 422 ASP cc_start: 0.7891 (m-30) cc_final: 0.7568 (m-30) REVERT: W 438 LYS cc_start: 0.7995 (tppp) cc_final: 0.7619 (tppp) REVERT: W 443 ASN cc_start: 0.6738 (m110) cc_final: 0.6450 (m-40) REVERT: X 77 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6391 (pp) REVERT: X 132 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7334 (ttm-80) REVERT: X 138 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7174 (tm-30) REVERT: X 150 GLU cc_start: 0.7523 (tp30) cc_final: 0.7309 (mm-30) REVERT: X 171 LYS cc_start: 0.7953 (tttt) cc_final: 0.7672 (tppt) REVERT: X 187 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7118 (tm-30) REVERT: X 210 LYS cc_start: 0.7289 (ptmt) cc_final: 0.6952 (ptmt) REVERT: X 228 GLU cc_start: 0.6775 (pt0) cc_final: 0.6311 (pt0) REVERT: X 240 LYS cc_start: 0.8298 (mtmt) cc_final: 0.8047 (mmmm) REVERT: X 282 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6682 (tp30) REVERT: X 290 LYS cc_start: 0.7650 (ttmm) cc_final: 0.7293 (mtmt) REVERT: X 315 MET cc_start: 0.7865 (mmp) cc_final: 0.7553 (mmm) REVERT: X 317 ASP cc_start: 0.6665 (OUTLIER) cc_final: 0.6344 (p0) REVERT: X 432 LYS cc_start: 0.8526 (mmmt) cc_final: 0.8245 (mmmm) REVERT: X 434 ILE cc_start: 0.7334 (mt) cc_final: 0.6975 (tt) REVERT: X 438 ASP cc_start: 0.7874 (m-30) cc_final: 0.7643 (m-30) REVERT: Y 132 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7926 (mp0) REVERT: Y 144 GLN cc_start: 0.6706 (tt0) cc_final: 0.6210 (tt0) REVERT: Y 160 ILE cc_start: 0.7853 (tt) cc_final: 0.7532 (tp) REVERT: Y 164 ASP cc_start: 0.7716 (m-30) cc_final: 0.7503 (m-30) REVERT: Y 169 TYR cc_start: 0.7636 (m-80) cc_final: 0.7037 (m-80) REVERT: Y 210 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7700 (mmm160) REVERT: Y 215 MET cc_start: 0.6692 (mtp) cc_final: 0.6293 (mtp) REVERT: Y 297 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7340 (mt-10) REVERT: Y 317 PHE cc_start: 0.8525 (m-80) cc_final: 0.8287 (m-80) REVERT: Y 361 GLU cc_start: 0.7151 (tt0) cc_final: 0.6924 (tp30) REVERT: Y 373 GLN cc_start: 0.7808 (tt0) cc_final: 0.7434 (mt0) REVERT: Y 378 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6741 (mm-30) REVERT: Y 415 ASN cc_start: 0.7293 (t0) cc_final: 0.6711 (t0) REVERT: Y 417 THR cc_start: 0.7535 (p) cc_final: 0.7066 (t) REVERT: Y 443 ASN cc_start: 0.7493 (m110) cc_final: 0.7074 (m110) REVERT: Y 444 GLU cc_start: 0.7535 (tt0) cc_final: 0.6985 (tp30) REVERT: Y 449 ASP cc_start: 0.7555 (t70) cc_final: 0.7069 (m-30) REVERT: Y 453 ASN cc_start: 0.7864 (m110) cc_final: 0.7543 (m-40) REVERT: Z 311 ARG cc_start: 0.7943 (ttm110) cc_final: 0.7621 (mtp85) REVERT: Z 314 GLU cc_start: 0.7881 (pt0) cc_final: 0.7662 (pt0) outliers start: 115 outliers final: 88 residues processed: 969 average time/residue: 0.4559 time to fit residues: 666.6110 Evaluate side-chains 1006 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 907 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1103 ASP Chi-restraints excluded: chain Q residue 1134 GLU Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1267 ASP Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1301 LEU Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain R residue 750 THR Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 246 ASP Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 314 ASN Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 448 ASP Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 32 ASP Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 316 GLU Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain U residue 448 ILE Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 243 ILE Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 314 ASN Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain V residue 458 THR Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 346 ASP Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain W residue 429 LEU Chi-restraints excluded: chain W residue 444 GLU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 182 ASP Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 166 GLU Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 418 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 1.9990 chunk 333 optimal weight: 2.9990 chunk 304 optimal weight: 0.0570 chunk 324 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 254 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 292 optimal weight: 0.7980 chunk 306 optimal weight: 1.9990 chunk 323 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 666 ASN ** R 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 256 ASN T 440 ASN ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 360 ASN ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 289 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29102 Z= 0.186 Angle : 0.548 8.523 39373 Z= 0.266 Chirality : 0.042 0.198 4620 Planarity : 0.003 0.044 5040 Dihedral : 6.201 132.269 4004 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.51 % Allowed : 26.07 % Favored : 70.42 % 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: 0.35 (0.14), residues: 3618 helix: 1.07 (0.14), residues: 1471 sheet: 0.61 (0.20), residues: 667 loop : -0.74 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q1361 HIS 0.014 0.001 HIS V 165 PHE 0.017 0.001 PHE R 691 TYR 0.025 0.001 TYR Q1337 ARG 0.009 0.000 ARG X 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 917 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7057 (p0) REVERT: Q 1112 LYS cc_start: 0.8205 (mtpp) cc_final: 0.7902 (mtpp) REVERT: Q 1134 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7554 (mm-30) REVERT: Q 1139 GLU cc_start: 0.7245 (tp30) cc_final: 0.6553 (tp30) REVERT: Q 1142 ARG cc_start: 0.7130 (ttp-110) cc_final: 0.6811 (ptp90) REVERT: Q 1189 SER cc_start: 0.7888 (t) cc_final: 0.7479 (p) REVERT: Q 1208 ARG cc_start: 0.7843 (ttm170) cc_final: 0.7454 (tpp80) REVERT: Q 1255 TYR cc_start: 0.7705 (t80) cc_final: 0.7256 (t80) REVERT: Q 1287 SER cc_start: 0.8005 (m) cc_final: 0.7646 (t) REVERT: Q 1316 HIS cc_start: 0.7731 (m-70) cc_final: 0.6844 (m-70) REVERT: Q 1327 MET cc_start: 0.6115 (mmm) cc_final: 0.5889 (mmm) REVERT: Q 1331 MET cc_start: 0.7464 (mmm) cc_final: 0.7243 (mmm) REVERT: Q 1432 MET cc_start: 0.4606 (tpp) cc_final: 0.4136 (tpp) REVERT: R 65 ASN cc_start: 0.8302 (t0) cc_final: 0.7963 (t0) REVERT: R 79 PHE cc_start: 0.8092 (m-10) cc_final: 0.7770 (m-10) REVERT: R 85 ASP cc_start: 0.8798 (m-30) cc_final: 0.8537 (m-30) REVERT: R 93 ARG cc_start: 0.8546 (tmm-80) cc_final: 0.8155 (ttp-170) REVERT: R 95 GLN cc_start: 0.8928 (mt0) cc_final: 0.8614 (mt0) REVERT: R 97 ARG cc_start: 0.7906 (ttp-110) cc_final: 0.7652 (ttp-110) REVERT: R 144 GLN cc_start: 0.6725 (pt0) cc_final: 0.6483 (pt0) REVERT: R 146 GLN cc_start: 0.7766 (mm110) cc_final: 0.7494 (mm110) REVERT: R 192 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7340 (mm-30) REVERT: R 244 GLU cc_start: 0.7763 (tt0) cc_final: 0.7455 (tt0) REVERT: R 249 ASP cc_start: 0.8189 (m-30) cc_final: 0.7910 (m-30) REVERT: R 260 ASP cc_start: 0.7372 (m-30) cc_final: 0.6968 (m-30) REVERT: R 262 GLU cc_start: 0.7772 (mp0) cc_final: 0.7096 (mp0) REVERT: R 264 ILE cc_start: 0.8131 (tt) cc_final: 0.7737 (tp) REVERT: R 269 ASN cc_start: 0.7204 (t0) cc_final: 0.6603 (t0) REVERT: R 270 LEU cc_start: 0.8399 (mt) cc_final: 0.8137 (mm) REVERT: R 601 HIS cc_start: 0.7648 (t70) cc_final: 0.6967 (t-170) REVERT: R 608 GLU cc_start: 0.7574 (mt-10) cc_final: 0.6847 (tt0) REVERT: R 623 GLU cc_start: 0.8247 (tp30) cc_final: 0.8024 (tp30) REVERT: R 677 VAL cc_start: 0.8641 (t) cc_final: 0.8303 (m) REVERT: R 682 GLU cc_start: 0.8102 (mp0) cc_final: 0.7875 (mp0) REVERT: R 709 ASP cc_start: 0.7512 (m-30) cc_final: 0.7180 (m-30) REVERT: R 720 ASN cc_start: 0.7634 (t0) cc_final: 0.6712 (t0) REVERT: R 723 GLN cc_start: 0.7629 (mp10) cc_final: 0.6577 (mp10) REVERT: R 724 TYR cc_start: 0.7718 (t80) cc_final: 0.7259 (t80) REVERT: R 726 LYS cc_start: 0.8353 (mptt) cc_final: 0.8139 (mtmm) REVERT: R 736 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7109 (tm-30) REVERT: S 114 LYS cc_start: 0.7919 (mttp) cc_final: 0.7632 (mttp) REVERT: S 127 SER cc_start: 0.8438 (t) cc_final: 0.8045 (t) REVERT: T 99 LYS cc_start: 0.8000 (ttpp) cc_final: 0.7571 (ttmm) REVERT: T 105 LEU cc_start: 0.8031 (tp) cc_final: 0.7744 (tp) REVERT: T 122 MET cc_start: 0.7422 (tpt) cc_final: 0.7172 (mmm) REVERT: T 123 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6985 (mt-10) REVERT: T 134 LYS cc_start: 0.8456 (mtpp) cc_final: 0.8111 (mtmm) REVERT: T 182 ASP cc_start: 0.6544 (OUTLIER) cc_final: 0.6278 (p0) REVERT: T 195 SER cc_start: 0.7914 (m) cc_final: 0.7670 (t) REVERT: T 317 ASP cc_start: 0.7331 (t0) cc_final: 0.7045 (t0) REVERT: T 331 ASN cc_start: 0.8015 (m-40) cc_final: 0.7667 (m110) REVERT: T 365 ASP cc_start: 0.7712 (m-30) cc_final: 0.7326 (m-30) REVERT: T 385 GLU cc_start: 0.7742 (tt0) cc_final: 0.7312 (tm-30) REVERT: T 401 ASP cc_start: 0.7728 (m-30) cc_final: 0.7449 (p0) REVERT: T 430 ASN cc_start: 0.8307 (p0) cc_final: 0.8072 (p0) REVERT: T 441 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7344 (tp30) REVERT: U 65 THR cc_start: 0.7421 (p) cc_final: 0.7154 (t) REVERT: U 105 GLU cc_start: 0.8004 (tt0) cc_final: 0.7753 (tt0) REVERT: U 107 PHE cc_start: 0.8552 (m-80) cc_final: 0.8091 (m-80) REVERT: U 110 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7213 (pp20) REVERT: U 131 GLU cc_start: 0.7205 (pt0) cc_final: 0.6800 (pt0) REVERT: U 142 GLU cc_start: 0.6603 (tm-30) cc_final: 0.5691 (tm-30) REVERT: U 144 GLN cc_start: 0.6558 (OUTLIER) cc_final: 0.5532 (mp10) REVERT: U 157 LYS cc_start: 0.7684 (mttt) cc_final: 0.6937 (mtpt) REVERT: U 170 GLU cc_start: 0.7106 (tp30) cc_final: 0.6831 (tp30) REVERT: U 185 LEU cc_start: 0.8064 (mp) cc_final: 0.7667 (mp) REVERT: U 188 ASP cc_start: 0.7905 (m-30) cc_final: 0.7391 (m-30) REVERT: U 193 ASP cc_start: 0.7636 (t0) cc_final: 0.6939 (t0) REVERT: U 228 GLU cc_start: 0.7662 (mm-30) cc_final: 0.6803 (mm-30) REVERT: U 233 LYS cc_start: 0.7349 (mmmt) cc_final: 0.7009 (mmmt) REVERT: U 264 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7441 (mm-30) REVERT: U 281 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7649 (tttp) REVERT: U 282 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7167 (mt-10) REVERT: U 283 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6765 (mt-10) REVERT: U 339 SER cc_start: 0.8394 (m) cc_final: 0.8129 (t) REVERT: U 374 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7369 (mm-30) REVERT: U 451 GLN cc_start: 0.7305 (mm-40) cc_final: 0.7010 (mp10) REVERT: V 42 LYS cc_start: 0.7147 (mtmm) cc_final: 0.6254 (tttm) REVERT: V 99 LYS cc_start: 0.8196 (mtpt) cc_final: 0.7746 (mtpt) REVERT: V 109 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7629 (mt-10) REVERT: V 135 GLU cc_start: 0.7472 (tt0) cc_final: 0.7150 (tt0) REVERT: V 144 VAL cc_start: 0.7650 (t) cc_final: 0.7238 (m) REVERT: V 177 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7534 (ttpp) REVERT: V 193 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7566 (mtpt) REVERT: V 198 ASP cc_start: 0.7219 (m-30) cc_final: 0.6865 (m-30) REVERT: V 214 ARG cc_start: 0.7311 (mmt180) cc_final: 0.6610 (mmm-85) REVERT: V 227 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7284 (mm-30) REVERT: V 294 LYS cc_start: 0.7546 (tppt) cc_final: 0.7328 (tppt) REVERT: V 297 ASP cc_start: 0.7830 (t0) cc_final: 0.7526 (t0) REVERT: V 302 GLU cc_start: 0.7157 (pt0) cc_final: 0.6829 (pt0) REVERT: V 326 LYS cc_start: 0.7444 (tmmt) cc_final: 0.7093 (tppt) REVERT: V 355 SER cc_start: 0.8040 (m) cc_final: 0.7575 (t) REVERT: V 385 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7114 (mm-30) REVERT: V 394 GLN cc_start: 0.7672 (mt0) cc_final: 0.7218 (pt0) REVERT: V 454 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7813 (ttmm) REVERT: W 38 ARG cc_start: 0.7768 (mtm-85) cc_final: 0.7256 (mtt90) REVERT: W 167 THR cc_start: 0.8001 (p) cc_final: 0.7742 (t) REVERT: W 170 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7527 (mp0) REVERT: W 182 GLU cc_start: 0.7934 (tt0) cc_final: 0.7464 (tm-30) REVERT: W 193 ASP cc_start: 0.7495 (t0) cc_final: 0.7156 (t0) REVERT: W 204 ARG cc_start: 0.6955 (ttt90) cc_final: 0.6552 (ttt90) REVERT: W 266 ARG cc_start: 0.7149 (mtm-85) cc_final: 0.6547 (mtm-85) REVERT: W 302 ASP cc_start: 0.6986 (t0) cc_final: 0.6526 (t0) REVERT: W 304 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6818 (mp0) REVERT: W 327 ARG cc_start: 0.8214 (ttm170) cc_final: 0.7912 (ttm-80) REVERT: W 331 LYS cc_start: 0.8468 (tttp) cc_final: 0.8159 (mtpp) REVERT: W 338 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7861 (mttp) REVERT: W 376 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: W 378 GLU cc_start: 0.7961 (mp0) cc_final: 0.7239 (tm-30) REVERT: W 393 GLU cc_start: 0.7914 (tt0) cc_final: 0.7619 (mt-10) REVERT: W 413 ARG cc_start: 0.7637 (mtp180) cc_final: 0.7230 (mtm180) REVERT: W 422 ASP cc_start: 0.7884 (m-30) cc_final: 0.7563 (m-30) REVERT: W 438 LYS cc_start: 0.7971 (tppp) cc_final: 0.7594 (tppp) REVERT: W 443 ASN cc_start: 0.6758 (m110) cc_final: 0.6466 (m-40) REVERT: W 449 ASP cc_start: 0.7430 (t70) cc_final: 0.7113 (t70) REVERT: X 77 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6387 (pp) REVERT: X 132 ARG cc_start: 0.7886 (tpp80) cc_final: 0.7332 (ttm-80) REVERT: X 143 GLU cc_start: 0.7634 (tt0) cc_final: 0.7349 (tt0) REVERT: X 171 LYS cc_start: 0.7902 (tttt) cc_final: 0.7654 (tppt) REVERT: X 187 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7113 (tm-30) REVERT: X 210 LYS cc_start: 0.7305 (ptmt) cc_final: 0.6970 (ptmt) REVERT: X 228 GLU cc_start: 0.6774 (pt0) cc_final: 0.6353 (pt0) REVERT: X 240 LYS cc_start: 0.8318 (mtmt) cc_final: 0.8075 (mtmm) REVERT: X 276 LYS cc_start: 0.7485 (tttm) cc_final: 0.7064 (tmtt) REVERT: X 282 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6688 (tp30) REVERT: X 290 LYS cc_start: 0.7653 (ttmm) cc_final: 0.7293 (mtmt) REVERT: X 315 MET cc_start: 0.7858 (mmp) cc_final: 0.7545 (mmm) REVERT: X 317 ASP cc_start: 0.6675 (OUTLIER) cc_final: 0.6360 (p0) REVERT: X 385 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7488 (tt0) REVERT: X 432 LYS cc_start: 0.8538 (mmmt) cc_final: 0.8256 (mmmm) REVERT: X 434 ILE cc_start: 0.7313 (mt) cc_final: 0.6955 (tt) REVERT: X 438 ASP cc_start: 0.7876 (m-30) cc_final: 0.7645 (m-30) REVERT: Y 132 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7929 (mp0) REVERT: Y 144 GLN cc_start: 0.6675 (tt0) cc_final: 0.6186 (tt0) REVERT: Y 160 ILE cc_start: 0.7840 (tt) cc_final: 0.7559 (tp) REVERT: Y 210 ARG cc_start: 0.8168 (mmm160) cc_final: 0.7720 (mmm160) REVERT: Y 215 MET cc_start: 0.6721 (mtp) cc_final: 0.6306 (mtp) REVERT: Y 297 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7315 (mt-10) REVERT: Y 317 PHE cc_start: 0.8537 (m-80) cc_final: 0.8300 (m-80) REVERT: Y 373 GLN cc_start: 0.7812 (tt0) cc_final: 0.7463 (mt0) REVERT: Y 378 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6736 (mm-30) REVERT: Y 392 VAL cc_start: 0.7724 (t) cc_final: 0.7503 (p) REVERT: Y 415 ASN cc_start: 0.7291 (t0) cc_final: 0.6716 (t0) REVERT: Y 417 THR cc_start: 0.7544 (p) cc_final: 0.7076 (t) REVERT: Y 443 ASN cc_start: 0.7493 (m110) cc_final: 0.7077 (m110) REVERT: Y 444 GLU cc_start: 0.7545 (tt0) cc_final: 0.6994 (tp30) REVERT: Y 449 ASP cc_start: 0.7561 (t70) cc_final: 0.7074 (m-30) REVERT: Y 453 ASN cc_start: 0.7858 (m110) cc_final: 0.7561 (m-40) REVERT: Z 311 ARG cc_start: 0.7907 (ttm110) cc_final: 0.7585 (mtp85) REVERT: Z 314 GLU cc_start: 0.7898 (pt0) cc_final: 0.7673 (pt0) outliers start: 111 outliers final: 88 residues processed: 973 average time/residue: 0.4554 time to fit residues: 670.8474 Evaluate side-chains 1002 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 904 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1103 ASP Chi-restraints excluded: chain Q residue 1134 GLU Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1267 ASP Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain R residue 750 THR Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 246 ASP Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 314 ASN Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 448 ASP Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 32 ASP Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 433 SER Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 227 GLU Chi-restraints excluded: chain V residue 243 ILE Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 314 ASN Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain V residue 458 THR Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 315 ASP Chi-restraints excluded: chain W residue 346 ASP Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain W residue 429 LEU Chi-restraints excluded: chain W residue 444 GLU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 182 ASP Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 166 GLU Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 418 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 1.9990 chunk 342 optimal weight: 0.5980 chunk 209 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 359 optimal weight: 1.9990 chunk 331 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 221 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 191 HIS R 666 ASN ** R 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 256 ASN T 440 ASN U 310 ASN ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN W 90 GLN W 360 ASN ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 256 ASN X 289 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29102 Z= 0.246 Angle : 0.576 9.469 39373 Z= 0.281 Chirality : 0.044 0.195 4620 Planarity : 0.003 0.037 5040 Dihedral : 6.304 131.118 4004 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.35 % Allowed : 26.00 % Favored : 70.64 % 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: 0.30 (0.14), residues: 3618 helix: 1.02 (0.14), residues: 1470 sheet: 0.60 (0.20), residues: 657 loop : -0.76 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q1361 HIS 0.012 0.001 HIS V 165 PHE 0.016 0.001 PHE R 691 TYR 0.025 0.001 TYR Q1337 ARG 0.010 0.000 ARG X 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 924 time to evaluate : 3.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7131 (p0) REVERT: Q 1112 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7935 (mtpp) REVERT: Q 1134 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7530 (mm-30) REVERT: Q 1139 GLU cc_start: 0.7288 (tp30) cc_final: 0.6068 (tp30) REVERT: Q 1142 ARG cc_start: 0.7136 (ttp-110) cc_final: 0.6774 (ptp90) REVERT: Q 1189 SER cc_start: 0.7885 (t) cc_final: 0.7489 (p) REVERT: Q 1208 ARG cc_start: 0.7869 (ttm170) cc_final: 0.7494 (tpp80) REVERT: Q 1255 TYR cc_start: 0.7728 (t80) cc_final: 0.7354 (t80) REVERT: Q 1287 SER cc_start: 0.8048 (m) cc_final: 0.7682 (t) REVERT: Q 1316 HIS cc_start: 0.7755 (m-70) cc_final: 0.6810 (m-70) REVERT: Q 1327 MET cc_start: 0.6199 (mmm) cc_final: 0.5984 (mmm) REVERT: Q 1331 MET cc_start: 0.7488 (mmm) cc_final: 0.7282 (mmm) REVERT: R 65 ASN cc_start: 0.8312 (t0) cc_final: 0.8081 (t0) REVERT: R 79 PHE cc_start: 0.8098 (m-10) cc_final: 0.7772 (m-10) REVERT: R 85 ASP cc_start: 0.8780 (m-30) cc_final: 0.8505 (m-30) REVERT: R 93 ARG cc_start: 0.8551 (tmm-80) cc_final: 0.8140 (ttp-170) REVERT: R 95 GLN cc_start: 0.8925 (mt0) cc_final: 0.8613 (mt0) REVERT: R 97 ARG cc_start: 0.7876 (ttp-110) cc_final: 0.7625 (ttp-110) REVERT: R 144 GLN cc_start: 0.6746 (pt0) cc_final: 0.6525 (pt0) REVERT: R 146 GLN cc_start: 0.7824 (mm110) cc_final: 0.7573 (mm110) REVERT: R 191 HIS cc_start: 0.7706 (t70) cc_final: 0.7496 (t-90) REVERT: R 192 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7346 (mm-30) REVERT: R 244 GLU cc_start: 0.7814 (tt0) cc_final: 0.7510 (tt0) REVERT: R 249 ASP cc_start: 0.8107 (m-30) cc_final: 0.7819 (m-30) REVERT: R 260 ASP cc_start: 0.7393 (m-30) cc_final: 0.6993 (m-30) REVERT: R 262 GLU cc_start: 0.7739 (mp0) cc_final: 0.7074 (mp0) REVERT: R 264 ILE cc_start: 0.8130 (tt) cc_final: 0.7751 (tp) REVERT: R 269 ASN cc_start: 0.7270 (t0) cc_final: 0.6653 (t0) REVERT: R 270 LEU cc_start: 0.8421 (mt) cc_final: 0.8156 (mm) REVERT: R 601 HIS cc_start: 0.7632 (t70) cc_final: 0.6968 (t-170) REVERT: R 608 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6804 (tt0) REVERT: R 612 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.6925 (mpp) REVERT: R 677 VAL cc_start: 0.8672 (t) cc_final: 0.8333 (m) REVERT: R 709 ASP cc_start: 0.7551 (m-30) cc_final: 0.7176 (m-30) REVERT: R 720 ASN cc_start: 0.7694 (t0) cc_final: 0.6778 (t0) REVERT: R 723 GLN cc_start: 0.7661 (mp10) cc_final: 0.6579 (mp10) REVERT: R 724 TYR cc_start: 0.7763 (t80) cc_final: 0.7327 (t80) REVERT: R 726 LYS cc_start: 0.8350 (mptt) cc_final: 0.8139 (mtmm) REVERT: R 736 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7125 (tm-30) REVERT: R 744 GLU cc_start: 0.7935 (tp30) cc_final: 0.7564 (tp30) REVERT: S 114 LYS cc_start: 0.7923 (mttp) cc_final: 0.7625 (mttp) REVERT: S 127 SER cc_start: 0.8472 (t) cc_final: 0.8112 (t) REVERT: T 99 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7573 (ttmm) REVERT: T 105 LEU cc_start: 0.8045 (tp) cc_final: 0.7740 (tp) REVERT: T 122 MET cc_start: 0.7410 (tpt) cc_final: 0.7175 (mmm) REVERT: T 123 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6991 (mt-10) REVERT: T 134 LYS cc_start: 0.8422 (mtpp) cc_final: 0.8061 (mtmm) REVERT: T 195 SER cc_start: 0.7891 (m) cc_final: 0.7644 (t) REVERT: T 317 ASP cc_start: 0.7326 (t0) cc_final: 0.7043 (t0) REVERT: T 331 ASN cc_start: 0.8008 (m-40) cc_final: 0.7640 (m110) REVERT: T 365 ASP cc_start: 0.7724 (m-30) cc_final: 0.7324 (m-30) REVERT: T 385 GLU cc_start: 0.7745 (tt0) cc_final: 0.7341 (tm-30) REVERT: T 401 ASP cc_start: 0.7738 (m-30) cc_final: 0.7439 (p0) REVERT: T 430 ASN cc_start: 0.8293 (p0) cc_final: 0.8063 (p0) REVERT: T 441 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7361 (tp30) REVERT: U 65 THR cc_start: 0.7470 (p) cc_final: 0.7234 (t) REVERT: U 105 GLU cc_start: 0.7985 (tt0) cc_final: 0.7715 (tt0) REVERT: U 107 PHE cc_start: 0.8555 (m-80) cc_final: 0.8081 (m-80) REVERT: U 110 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7173 (pp20) REVERT: U 131 GLU cc_start: 0.7201 (pt0) cc_final: 0.6792 (pt0) REVERT: U 142 GLU cc_start: 0.6638 (tm-30) cc_final: 0.5788 (tm-30) REVERT: U 144 GLN cc_start: 0.6517 (OUTLIER) cc_final: 0.5454 (mp10) REVERT: U 157 LYS cc_start: 0.7712 (mttt) cc_final: 0.6790 (mtpt) REVERT: U 170 GLU cc_start: 0.7137 (tp30) cc_final: 0.6852 (tp30) REVERT: U 185 LEU cc_start: 0.8055 (mp) cc_final: 0.7691 (mp) REVERT: U 188 ASP cc_start: 0.7981 (m-30) cc_final: 0.7462 (m-30) REVERT: U 193 ASP cc_start: 0.7557 (t0) cc_final: 0.6834 (t0) REVERT: U 228 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7263 (mm-30) REVERT: U 233 LYS cc_start: 0.7344 (mmmt) cc_final: 0.7015 (mmmt) REVERT: U 264 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7570 (tt0) REVERT: U 281 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7668 (tttp) REVERT: U 282 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7227 (mt-10) REVERT: U 283 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6868 (mt-10) REVERT: U 339 SER cc_start: 0.8433 (m) cc_final: 0.8173 (t) REVERT: U 374 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7367 (mm-30) REVERT: U 444 GLU cc_start: 0.7558 (pt0) cc_final: 0.7139 (mt-10) REVERT: U 451 GLN cc_start: 0.7306 (mm-40) cc_final: 0.7004 (mp10) REVERT: V 42 LYS cc_start: 0.7063 (mtmm) cc_final: 0.6196 (tttm) REVERT: V 69 LYS cc_start: 0.7928 (mttm) cc_final: 0.7400 (mtpp) REVERT: V 99 LYS cc_start: 0.8236 (mtpt) cc_final: 0.7793 (mtpt) REVERT: V 109 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7666 (mt-10) REVERT: V 135 GLU cc_start: 0.7495 (tt0) cc_final: 0.7198 (tt0) REVERT: V 144 VAL cc_start: 0.7641 (t) cc_final: 0.7215 (m) REVERT: V 177 LYS cc_start: 0.7989 (ttmt) cc_final: 0.7534 (ttpp) REVERT: V 193 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7597 (mtpt) REVERT: V 198 ASP cc_start: 0.7304 (m-30) cc_final: 0.6950 (m-30) REVERT: V 214 ARG cc_start: 0.7291 (mmt180) cc_final: 0.6620 (mmm-85) REVERT: V 294 LYS cc_start: 0.7581 (tppt) cc_final: 0.7354 (tppt) REVERT: V 297 ASP cc_start: 0.7818 (t0) cc_final: 0.7519 (t0) REVERT: V 302 GLU cc_start: 0.7153 (pt0) cc_final: 0.6804 (pt0) REVERT: V 326 LYS cc_start: 0.7464 (tmmt) cc_final: 0.7127 (tppt) REVERT: V 355 SER cc_start: 0.8077 (m) cc_final: 0.7628 (t) REVERT: V 385 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7127 (mm-30) REVERT: V 394 GLN cc_start: 0.7668 (mt0) cc_final: 0.7115 (pt0) REVERT: V 454 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7817 (ttmm) REVERT: W 38 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7263 (mtt90) REVERT: W 167 THR cc_start: 0.7997 (p) cc_final: 0.7734 (t) REVERT: W 170 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7502 (mp0) REVERT: W 182 GLU cc_start: 0.7966 (tt0) cc_final: 0.7465 (tm-30) REVERT: W 204 ARG cc_start: 0.6936 (ttt90) cc_final: 0.6516 (ttt90) REVERT: W 266 ARG cc_start: 0.7160 (mtm-85) cc_final: 0.6535 (mtm-85) REVERT: W 302 ASP cc_start: 0.7043 (t0) cc_final: 0.6559 (t0) REVERT: W 304 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6813 (mp0) REVERT: W 327 ARG cc_start: 0.8215 (ttm170) cc_final: 0.7901 (ttm-80) REVERT: W 331 LYS cc_start: 0.8467 (tttp) cc_final: 0.8146 (mtpp) REVERT: W 338 LYS cc_start: 0.8120 (mtpt) cc_final: 0.7838 (mttm) REVERT: W 376 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: W 378 GLU cc_start: 0.7992 (mp0) cc_final: 0.7284 (tm-30) REVERT: W 393 GLU cc_start: 0.7927 (tt0) cc_final: 0.7621 (mt-10) REVERT: W 413 ARG cc_start: 0.7671 (mtp180) cc_final: 0.7244 (mtm180) REVERT: W 422 ASP cc_start: 0.7872 (m-30) cc_final: 0.7547 (m-30) REVERT: W 438 LYS cc_start: 0.7969 (tppp) cc_final: 0.7587 (tppp) REVERT: W 443 ASN cc_start: 0.6833 (m110) cc_final: 0.6549 (m-40) REVERT: W 449 ASP cc_start: 0.7453 (t70) cc_final: 0.7148 (t70) REVERT: X 77 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6457 (pt) REVERT: X 132 ARG cc_start: 0.7875 (tpp80) cc_final: 0.7334 (ttm-80) REVERT: X 171 LYS cc_start: 0.7944 (tttt) cc_final: 0.7648 (tppt) REVERT: X 187 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7117 (tm-30) REVERT: X 210 LYS cc_start: 0.7317 (ptmt) cc_final: 0.6978 (ptmt) REVERT: X 228 GLU cc_start: 0.6776 (pt0) cc_final: 0.6351 (pt0) REVERT: X 240 LYS cc_start: 0.8344 (mtmt) cc_final: 0.8108 (mtmm) REVERT: X 276 LYS cc_start: 0.7520 (tttm) cc_final: 0.7075 (tmtt) REVERT: X 282 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6691 (tp30) REVERT: X 290 LYS cc_start: 0.7657 (ttmm) cc_final: 0.7299 (mtmt) REVERT: X 315 MET cc_start: 0.7935 (mmp) cc_final: 0.7629 (mmm) REVERT: X 317 ASP cc_start: 0.6771 (OUTLIER) cc_final: 0.6481 (p0) REVERT: X 385 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7450 (tt0) REVERT: X 432 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8277 (mmmm) REVERT: X 434 ILE cc_start: 0.7295 (mt) cc_final: 0.6935 (tt) REVERT: X 438 ASP cc_start: 0.7882 (m-30) cc_final: 0.7650 (m-30) REVERT: Y 132 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7932 (mp0) REVERT: Y 144 GLN cc_start: 0.6679 (tt0) cc_final: 0.6188 (tt0) REVERT: Y 210 ARG cc_start: 0.8181 (mmm160) cc_final: 0.7750 (mmm160) REVERT: Y 215 MET cc_start: 0.6842 (mtp) cc_final: 0.6598 (mtp) REVERT: Y 297 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7335 (mt-10) REVERT: Y 317 PHE cc_start: 0.8558 (m-80) cc_final: 0.8326 (m-80) REVERT: Y 373 GLN cc_start: 0.7822 (tt0) cc_final: 0.7461 (mt0) REVERT: Y 378 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6694 (mm-30) REVERT: Y 415 ASN cc_start: 0.7327 (t0) cc_final: 0.6751 (t0) REVERT: Y 417 THR cc_start: 0.7576 (p) cc_final: 0.7094 (t) REVERT: Y 443 ASN cc_start: 0.7480 (m110) cc_final: 0.7085 (m110) REVERT: Y 444 GLU cc_start: 0.7599 (tt0) cc_final: 0.7041 (tp30) REVERT: Y 449 ASP cc_start: 0.7570 (t70) cc_final: 0.7081 (m-30) REVERT: Y 453 ASN cc_start: 0.7868 (m110) cc_final: 0.7623 (m-40) REVERT: Z 311 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7560 (mtp85) REVERT: Z 314 GLU cc_start: 0.7932 (pt0) cc_final: 0.7720 (pt0) outliers start: 106 outliers final: 86 residues processed: 977 average time/residue: 0.4544 time to fit residues: 671.0950 Evaluate side-chains 1015 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 920 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1103 ASP Chi-restraints excluded: chain Q residue 1134 GLU Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1267 ASP Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1301 LEU Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 612 MET Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain R residue 750 THR Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 246 ASP Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 314 ASN Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 438 ASP Chi-restraints excluded: chain T residue 448 ASP Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 32 ASP Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 433 SER Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 243 ILE Chi-restraints excluded: chain V residue 314 ASN Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain V residue 400 LEU Chi-restraints excluded: chain V residue 429 SER Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 315 ASP Chi-restraints excluded: chain W residue 346 ASP Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain W residue 429 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 182 ASP Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 418 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 3.9990 chunk 305 optimal weight: 0.0000 chunk 87 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 294 optimal weight: 0.9980 chunk 36 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 666 ASN ** R 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 256 ASN T 440 ASN U 310 ASN ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 256 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.120564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099769 restraints weight = 45901.861| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.27 r_work: 0.3170 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29102 Z= 0.300 Angle : 0.606 11.226 39373 Z= 0.297 Chirality : 0.045 0.201 4620 Planarity : 0.004 0.052 5040 Dihedral : 6.421 132.032 4004 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.35 % Allowed : 26.48 % Favored : 70.17 % 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 (0.14), residues: 3618 helix: 0.92 (0.14), residues: 1475 sheet: 0.57 (0.20), residues: 663 loop : -0.80 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q1396 HIS 0.018 0.002 HIS R 121 PHE 0.017 0.001 PHE R 691 TYR 0.024 0.002 TYR Q1337 ARG 0.010 0.000 ARG X 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11509.00 seconds wall clock time: 205 minutes 12.76 seconds (12312.76 seconds total)