Starting phenix.real_space_refine on Tue Feb 20 18:57:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etw_28601/02_2024/8etw_28601_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etw_28601/02_2024/8etw_28601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etw_28601/02_2024/8etw_28601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etw_28601/02_2024/8etw_28601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etw_28601/02_2024/8etw_28601_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etw_28601/02_2024/8etw_28601_neut_updated.pdb" } resolution = 2.64 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= 0.023 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 18039 2.51 5 N 4942 2.21 5 O 5578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q ASP 1072": "OD1" <-> "OD2" Residue "Q TYR 1083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 1103": "OD1" <-> "OD2" Residue "Q TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 1167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "R PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 201": "OD1" <-> "OD2" Residue "R ASP 585": "OD1" <-> "OD2" Residue "R ASP 602": "OD1" <-> "OD2" Residue "R GLU 623": "OE1" <-> "OE2" Residue "R ASP 634": "OD1" <-> "OD2" Residue "R GLU 643": "OE1" <-> "OE2" Residue "R ASP 663": "OD1" <-> "OD2" Residue "R PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 95": "OE1" <-> "OE2" Residue "T GLU 119": "OE1" <-> "OE2" Residue "T GLU 203": "OE1" <-> "OE2" Residue "T GLU 225": "OE1" <-> "OE2" Residue "T GLU 227": "OE1" <-> "OE2" Residue "T GLU 242": "OE1" <-> "OE2" Residue "T ASP 253": "OD1" <-> "OD2" Residue "T GLU 279": "OE1" <-> "OE2" Residue "T GLU 287": "OE1" <-> "OE2" Residue "T TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 365": "OD1" <-> "OD2" Residue "T GLU 385": "OE1" <-> "OE2" Residue "T ASP 401": "OD1" <-> "OD2" Residue "T GLU 433": "OE1" <-> "OE2" Residue "T ASP 448": "OD1" <-> "OD2" Residue "U PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 115": "OE1" <-> "OE2" Residue "U ASP 193": "OD1" <-> "OD2" Residue "U PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 271": "OD1" <-> "OD2" Residue "U GLU 304": "OE1" <-> "OE2" Residue "U ASP 349": "OD1" <-> "OD2" Residue "U TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 374": "OE1" <-> "OE2" Residue "U GLU 375": "OE1" <-> "OE2" Residue "U ASP 385": "OD1" <-> "OD2" Residue "U GLU 442": "OE1" <-> "OE2" Residue "U TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 135": "OE1" <-> "OE2" Residue "V GLU 141": "OE1" <-> "OE2" Residue "V GLU 146": "OE1" <-> "OE2" Residue "V GLU 150": "OE1" <-> "OE2" Residue "V TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 198": "OD1" <-> "OD2" Residue "V GLU 203": "OE1" <-> "OE2" Residue "V ASP 223": "OD1" <-> "OD2" Residue "V ASP 251": "OD1" <-> "OD2" Residue "V GLU 312": "OE1" <-> "OE2" Residue "V TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 365": "OD1" <-> "OD2" Residue "V ASP 376": "OD1" <-> "OD2" Residue "V PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 448": "OD1" <-> "OD2" Residue "V GLU 457": "OE1" <-> "OE2" Residue "W PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 142": "OE1" <-> "OE2" Residue "W GLU 166": "OE1" <-> "OE2" Residue "W ASP 193": "OD1" <-> "OD2" Residue "W ASP 245": "OD1" <-> "OD2" Residue "W ASP 271": "OD1" <-> "OD2" Residue "W ASP 296": "OD1" <-> "OD2" Residue "W ASP 302": "OD1" <-> "OD2" Residue "W ASP 349": "OD1" <-> "OD2" Residue "W GLU 375": "OE1" <-> "OE2" Residue "W GLU 419": "OE1" <-> "OE2" Residue "W GLU 442": "OE1" <-> "OE2" Residue "W TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 450": "OD1" <-> "OD2" Residue "X ASP 36": "OD1" <-> "OD2" Residue "X GLU 45": "OE1" <-> "OE2" Residue "X GLU 119": "OE1" <-> "OE2" Residue "X PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 141": "OE1" <-> "OE2" Residue "X ASP 216": "OD1" <-> "OD2" Residue "X GLU 221": "OE1" <-> "OE2" Residue "X ASP 223": "OD1" <-> "OD2" Residue "X GLU 242": "OE1" <-> "OE2" Residue "X GLU 385": "OE1" <-> "OE2" Residue "X GLU 441": "OE1" <-> "OE2" Residue "Y GLU 131": "OE1" <-> "OE2" Residue "Y ASP 164": "OD1" <-> "OD2" Residue "Y GLU 170": "OE1" <-> "OE2" Residue "Y ASP 213": "OD1" <-> "OD2" Residue "Y GLU 243": "OE1" <-> "OE2" Residue "Y GLU 314": "OE1" <-> "OE2" Residue "Y PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 450": "OD1" <-> "OD2" Residue "Z PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 303": "OE1" <-> "OE2" Residue "Z GLU 313": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28666 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: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3350 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 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: 14.00, per 1000 atoms: 0.49 Number of scatterers: 28666 At special positions: 0 Unit cell: (128.59, 158.65, 197.06, 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 5578 8.00 N 4942 7.00 C 18039 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: 9.65 Conformation dependent library (CDL) restraints added in 4.7 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: 151 helices and 30 sheets defined 38.3% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.88 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 1001 through 1012 removed outlier: 3.960A pdb=" N GLN Q1006 " --> pdb=" O ASN Q1002 " (cutoff:3.500A) removed outlier: 3.844A 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 Processing helix chain 'Q' and resid 1148 through 1153 Processing helix chain 'Q' and resid 1170 through 1179 removed outlier: 3.605A pdb=" N VAL Q1177 " --> pdb=" O GLU Q1173 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR Q1178 " --> pdb=" O LEU Q1174 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG Q1179 " --> pdb=" O LEU Q1175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1186 through 1190 Processing helix chain 'Q' and resid 1193 through 1200 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: 3.827A pdb=" N VAL Q1309 " --> pdb=" O ASP Q1305 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS Q1310 " --> pdb=" O GLU Q1306 " (cutoff:3.500A) removed outlier: 3.618A 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 1358 through 1363 Processing helix chain 'Q' and resid 1398 through 1407 removed outlier: 3.701A 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 85 No H-bonds generated for 'chain 'R' and resid 83 through 85' 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 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 261 removed outlier: 3.504A pdb=" N ILE R 261 " --> pdb=" O TYR R 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 257 through 261' 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 595 Processing helix chain 'R' and resid 607 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: 3.845A 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 638 through 647 Processing helix chain 'R' and resid 659 through 667 removed outlier: 3.771A pdb=" N ASN R 667 " --> pdb=" O ASP R 663 " (cutoff:3.500A) Processing helix chain 'R' and resid 673 through 675 No H-bonds generated for 'chain 'R' and resid 673 through 675' Processing helix chain 'R' and resid 680 through 691 Processing helix chain 'R' and resid 709 through 719 Processing helix chain 'R' and resid 721 through 724 No H-bonds generated for 'chain 'R' and resid 721 through 724' Processing helix chain 'R' and resid 731 through 737 Processing helix chain 'S' and resid 29 through 39 removed outlier: 4.323A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL S 36 " --> pdb=" O PHE S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 82 removed outlier: 4.076A pdb=" N ILE S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 3.654A 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 142 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: 3.805A 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: 3.925A 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 255 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 327 removed outlier: 3.827A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (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 366 removed outlier: 3.661A pdb=" N ASP T 365 " --> pdb=" O PRO T 361 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG T 366 " --> pdb=" O ASP T 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 361 through 366' 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: 3.516A pdb=" N LEU T 416 " --> pdb=" O LEU T 412 " (cutoff:3.500A) removed outlier: 4.731A 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: 3.987A 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: 4.001A 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 312 removed outlier: 3.779A 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 349 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 413 removed outlier: 4.217A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE U 409 " --> pdb=" O VAL U 405 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG U 413 " --> pdb=" O ILE U 409 " (cutoff:3.500A) Processing helix chain 'U' and resid 420 through 429 Processing helix chain 'U' and resid 433 through 446 removed outlier: 6.716A pdb=" N SER U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLN U 446 " --> pdb=" O GLU U 442 " (cutoff:3.500A) 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: 3.856A 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: 3.694A 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: 3.777A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) removed outlier: 4.400A 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 366 removed outlier: 4.524A pdb=" N ARG V 366 " --> pdb=" O ASP V 362 " (cutoff:3.500A) 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 429 removed outlier: 4.292A pdb=" N LEU V 419 " --> pdb=" O ALA V 415 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA V 420 " --> pdb=" O LEU V 416 " (cutoff:3.500A) Proline residue: V 421 - end of helix removed outlier: 3.831A 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 92 Processing helix chain 'W' and resid 113 through 124 removed outlier: 4.055A 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: 4.112A 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 314 removed outlier: 3.936A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU W 314 " --> pdb=" O ASN W 310 " (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: 4.028A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (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: 3.692A 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: 3.795A pdb=" N ALA X 128 " --> pdb=" O ASN X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 183 through 192 removed outlier: 4.068A pdb=" N GLU X 187 " --> pdb=" O THR X 184 " (cutoff:3.500A) removed outlier: 3.650A 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: 4.478A 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: 3.869A 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 48 through 63 Processing helix chain 'Y' and resid 81 through 91 Processing helix chain 'Y' and resid 103 through 106 removed outlier: 4.014A pdb=" N ILE Y 106 " --> pdb=" O GLY Y 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 103 through 106' Processing helix chain 'Y' and resid 113 through 124 removed outlier: 3.853A 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 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 312 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 413 removed outlier: 3.857A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG Y 413 " --> pdb=" O ILE Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 420 through 429 Processing helix chain 'Y' and resid 433 through 441 Processing helix chain 'Y' and resid 444 through 446 No H-bonds generated for 'chain 'Y' and resid 444 through 446' Processing sheet with id= A, first strand: chain 'Q' and resid 949 through 954 removed outlier: 6.441A pdb=" N VAL Q1419 " --> pdb=" O ILE Q 950 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL Q 952 " --> pdb=" O VAL Q1419 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG Q1421 " --> pdb=" O VAL Q 952 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N CYS Q 954 " --> pdb=" O ARG Q1421 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU Q1423 " --> pdb=" O CYS Q 954 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'Q' and resid 1082 through 1084 removed outlier: 6.819A pdb=" N THR Q1220 " --> pdb=" O TYR Q1083 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'R' and resid 40 through 44 Processing sheet with id= D, first strand: chain 'R' and resid 67 through 71 Processing sheet with id= E, first strand: chain 'R' and resid 134 through 137 removed outlier: 3.771A pdb=" N THR R 164 " --> pdb=" O ILE R 134 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU R 136 " --> pdb=" O THR R 164 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'R' and resid 700 through 702 removed outlier: 6.877A pdb=" N VAL R 668 " --> pdb=" O ASN R 701 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU R 185 " --> pdb=" O LEU R 669 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR R 671 " --> pdb=" O LEU R 185 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE R 187 " --> pdb=" O THR R 671 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 198 through 200 Processing sheet with id= H, first strand: chain 'R' and resid 275 through 278 Processing sheet with id= I, first strand: chain 'T' and resid 367 through 371 removed outlier: 7.146A pdb=" N ALA T 74 " --> pdb=" O LEU T 368 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL T 336 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU T 77 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU T 338 " --> pdb=" O LEU T 77 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'T' and resid 301 through 305 Processing sheet with id= K, first strand: chain 'T' and resid 175 through 181 removed outlier: 3.586A pdb=" N GLY T 175 " --> pdb=" O SER T 172 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS T 165 " --> pdb=" O GLU T 150 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU T 146 " --> pdb=" O GLY T 169 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LYS T 171 " --> pdb=" O VAL T 144 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL T 144 " --> pdb=" O LYS T 171 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP T 198 " --> pdb=" O VAL T 144 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR T 201 " --> pdb=" O ARG T 211 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ARG T 211 " --> pdb=" O TYR T 201 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLU T 203 " --> pdb=" O VAL T 209 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL T 209 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 344 through 346 Processing sheet with id= M, first strand: chain 'U' and resid 351 through 355 removed outlier: 6.948A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL U 321 " --> pdb=" O VAL U 71 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL U 73 " --> pdb=" O VAL U 321 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET U 323 " --> pdb=" O VAL U 73 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'U' and resid 287 through 290 Processing sheet with id= O, first strand: chain 'U' and resid 166 through 171 removed outlier: 4.355A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS U 161 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL U 140 " --> pdb=" O LYS U 161 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP U 188 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER U 191 " --> pdb=" O LYS U 201 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LYS U 201 " --> pdb=" O SER U 191 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASP U 193 " --> pdb=" O ILE U 199 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE U 199 " --> pdb=" O ASP U 193 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'V' and resid 367 through 372 removed outlier: 7.185A pdb=" N ALA V 74 " --> pdb=" O LEU V 368 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU V 76 " --> pdb=" O VAL V 370 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR V 372 " --> pdb=" O LEU V 76 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA V 78 " --> pdb=" O THR V 372 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL V 336 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU V 77 " --> pdb=" O VAL V 336 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU V 338 " --> pdb=" O LEU V 77 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLY V 79 " --> pdb=" O LEU V 338 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N SER V 340 " --> pdb=" O GLY V 79 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V' and resid 301 through 305 Processing sheet with id= R, first strand: chain 'V' and resid 175 through 181 removed outlier: 3.692A pdb=" N GLY V 175 " --> pdb=" O SER V 172 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS V 165 " --> pdb=" O GLU V 150 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU V 146 " --> pdb=" O GLY V 169 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS V 171 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL V 144 " --> pdb=" O LYS V 171 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP V 198 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY V 213 " --> pdb=" O VAL V 199 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR V 201 " --> pdb=" O ARG V 211 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ARG V 211 " --> pdb=" O TYR V 201 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLU V 203 " --> pdb=" O VAL V 209 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL V 209 " --> pdb=" O GLU V 203 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'W' and resid 351 through 356 removed outlier: 6.808A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR W 356 " --> pdb=" O LEU W 72 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA W 74 " --> pdb=" O THR W 356 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL W 321 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL W 73 " --> pdb=" O VAL W 321 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N MET W 323 " --> pdb=" O VAL W 73 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N GLY W 75 " --> pdb=" O MET W 323 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR W 325 " --> pdb=" O GLY W 75 " (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: 3.817A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP W 188 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY W 203 " --> pdb=" O VAL W 189 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER W 191 " --> pdb=" O LYS W 201 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LYS W 201 " --> pdb=" O SER W 191 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ASP W 193 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 5.945A 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 372 removed outlier: 7.160A pdb=" N ALA X 74 " --> pdb=" O LEU X 368 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N THR X 372 " --> pdb=" O LEU X 76 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA X 78 " --> pdb=" O THR X 372 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL X 336 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU X 77 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU X 338 " --> pdb=" O LEU X 77 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLY X 79 " --> pdb=" O LEU X 338 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER X 340 " --> pdb=" O GLY X 79 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 301 through 305 Processing sheet with id= X, first strand: chain 'X' and resid 199 through 203 removed outlier: 6.446A pdb=" N GLY X 169 " --> pdb=" O THR X 145 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU X 147 " --> pdb=" O ILE X 167 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE X 167 " --> pdb=" O LEU X 147 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N HIS X 165 " --> pdb=" O PRO X 149 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL X 166 " --> pdb=" O LEU X 181 " (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 356 removed outlier: 3.505A pdb=" N ILE Y 352 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Y' and resid 286 through 290 Processing sheet with id= AB, first strand: chain 'Y' and resid 166 through 171 removed outlier: 3.641A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU Y 142 " --> pdb=" O THR Y 159 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS Y 161 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL Y 140 " --> pdb=" O LYS Y 161 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP Y 188 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER Y 191 " --> pdb=" O LYS Y 201 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LYS Y 201 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASP Y 193 " --> pdb=" O ILE Y 199 " (cutoff:3.500A) removed outlier: 6.588A 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 1050 hydrogen bonds defined for protein. 3099 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: 10.43 Time building geometry restraints manager: 10.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9096 1.34 - 1.46: 5669 1.46 - 1.58: 14147 1.58 - 1.71: 20 1.71 - 1.83: 166 Bond restraints: 29098 Sorted by residual: bond pdb=" CB PRO R 27 " pdb=" CG PRO R 27 " ideal model delta sigma weight residual 1.492 1.656 -0.164 5.00e-02 4.00e+02 1.08e+01 bond pdb=" N GLU X 225 " pdb=" CA GLU X 225 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.16e-02 7.43e+03 8.54e+00 bond pdb=" N SER V 340 " pdb=" CA SER V 340 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.29e-02 6.01e+03 7.11e+00 bond pdb=" N ARG V 342 " pdb=" CA ARG V 342 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.21e-02 6.83e+03 6.64e+00 bond pdb=" N GLU R 617 " pdb=" CA GLU R 617 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.25e-02 6.40e+03 6.35e+00 ... (remaining 29093 not shown) Histogram of bond angle deviations from ideal: 91.80 - 100.69: 26 100.69 - 109.57: 3239 109.57 - 118.46: 20024 118.46 - 127.34: 15865 127.34 - 136.23: 214 Bond angle restraints: 39368 Sorted by residual: angle pdb=" CA PRO R 27 " pdb=" N PRO R 27 " pdb=" CD PRO R 27 " ideal model delta sigma weight residual 112.00 97.75 14.25 1.40e+00 5.10e-01 1.04e+02 angle pdb=" N MET V 344 " pdb=" CA MET V 344 " pdb=" C MET V 344 " ideal model delta sigma weight residual 107.28 91.80 15.48 1.75e+00 3.27e-01 7.83e+01 angle pdb=" N GLY V 343 " pdb=" CA GLY V 343 " pdb=" C GLY V 343 " ideal model delta sigma weight residual 113.18 133.54 -20.36 2.37e+00 1.78e-01 7.38e+01 angle pdb=" N MET V 344 " pdb=" CA MET V 344 " pdb=" CB MET V 344 " ideal model delta sigma weight residual 111.74 125.94 -14.20 1.69e+00 3.50e-01 7.06e+01 angle pdb=" C LEU U 19 " pdb=" N ILE U 20 " pdb=" CA ILE U 20 " ideal model delta sigma weight residual 121.97 133.82 -11.85 1.80e+00 3.09e-01 4.33e+01 ... (remaining 39363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.07: 17000 33.07 - 66.15: 813 66.15 - 99.22: 53 99.22 - 132.29: 6 132.29 - 165.37: 5 Dihedral angle restraints: 17877 sinusoidal: 7315 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 300.00 134.64 165.37 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O1B ADP T 501 " pdb=" O3A ADP T 501 " pdb=" PB ADP T 501 " pdb=" PA ADP T 501 " ideal model delta sinusoidal sigma weight residual 300.00 140.64 159.36 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C5' ADP T 501 " pdb=" O5' ADP T 501 " pdb=" PA ADP T 501 " pdb=" O2A ADP T 501 " ideal model delta sinusoidal sigma weight residual 300.00 150.00 150.00 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 17874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3932 0.075 - 0.149: 637 0.149 - 0.224: 44 0.224 - 0.298: 4 0.298 - 0.373: 3 Chirality restraints: 4620 Sorted by residual: chirality pdb=" CG LEU Q 963 " pdb=" CB LEU Q 963 " pdb=" CD1 LEU Q 963 " pdb=" CD2 LEU Q 963 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB ILE Y 160 " pdb=" CA ILE Y 160 " pdb=" CG1 ILE Y 160 " pdb=" CG2 ILE Y 160 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CB THR U 40 " pdb=" CA THR U 40 " pdb=" OG1 THR U 40 " pdb=" CG2 THR U 40 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 4617 not shown) Planarity restraints: 5039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 58 " -0.089 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO R 59 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO R 59 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO R 59 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 599 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO R 600 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO R 600 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO R 600 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU U 182 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C GLU U 182 " 0.068 2.00e-02 2.50e+03 pdb=" O GLU U 182 " -0.026 2.00e-02 2.50e+03 pdb=" N LYS U 183 " -0.022 2.00e-02 2.50e+03 ... (remaining 5036 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 5 2.13 - 2.82: 8312 2.82 - 3.51: 36361 3.51 - 4.21: 65551 4.21 - 4.90: 115749 Nonbonded interactions: 225978 Sorted by model distance: nonbonded pdb=" OH TYR W 212 " pdb=" OD1 ASP X 182 " model vdw 1.435 2.440 nonbonded pdb=" CD2 LEU R 614 " pdb=" OE2 GLU R 617 " model vdw 1.666 3.460 nonbonded pdb=" NZ LYS Y 113 " pdb=" OD2 ASP Y 302 " model vdw 1.725 2.520 nonbonded pdb=" NH2 ARG Q1142 " pdb=" CB GLU Y 182 " model vdw 1.888 3.520 nonbonded pdb=" OH TYR W 212 " pdb=" CG ASP X 182 " model vdw 2.070 3.270 ... (remaining 225973 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 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 210 or resid 221 through 459 or \ resid 501)) selection = (chain 'Y' and (resid 18 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 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: 4.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 23.440 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 70.830 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.005 0.164 29098 Z= 0.340 Angle : 0.910 20.362 39368 Z= 0.479 Chirality : 0.054 0.373 4620 Planarity : 0.007 0.131 5039 Dihedral : 18.081 165.365 11057 Min Nonbonded Distance : 1.435 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.09 % Allowed : 28.01 % Favored : 71.90 % Cbeta Deviations : 0.06 % 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: -1.81 (0.12), residues: 3618 helix: -1.54 (0.11), residues: 1493 sheet: 0.58 (0.20), residues: 649 loop : -1.51 (0.14), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Y 280 HIS 0.008 0.001 HIS T 250 PHE 0.046 0.002 PHE Q1167 TYR 0.050 0.002 TYR X 323 ARG 0.019 0.001 ARG S 73 *********************** 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 860 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 857 time to evaluate : 3.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1122 TYR cc_start: 0.8688 (t80) cc_final: 0.8275 (t80) REVERT: R 719 ARG cc_start: 0.7512 (mpp80) cc_final: 0.7246 (mpp80) REVERT: T 268 MET cc_start: 0.7590 (mmm) cc_final: 0.7382 (mpp) REVERT: V 341 ASN cc_start: 0.7519 (p0) cc_final: 0.7058 (p0) REVERT: Y 174 LYS cc_start: 0.7712 (mttp) cc_final: 0.7503 (mmtp) REVERT: Z 311 ARG cc_start: 0.7781 (mpp80) cc_final: 0.7436 (mtt-85) outliers start: 3 outliers final: 4 residues processed: 859 average time/residue: 1.6542 time to fit residues: 1623.5680 Evaluate side-chains 820 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 816 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 0.0010 chunk 273 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 146 optimal weight: 0.1980 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 210 optimal weight: 0.6980 chunk 327 optimal weight: 0.9980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1117 ASN ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN R 611 GLN U 63 ASN U 274 ASN U 310 ASN U 446 GLN V 190 GLN V 205 ASN V 394 GLN X 190 GLN X 256 ASN X 325 ASN ** Y 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 252 GLN Y 310 ASN Y 441 GLN Y 443 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 29098 Z= 0.220 Angle : 0.567 8.340 39368 Z= 0.284 Chirality : 0.043 0.204 4620 Planarity : 0.004 0.071 5039 Dihedral : 8.375 146.457 4010 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.08 % Allowed : 24.46 % Favored : 71.46 % 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: -0.72 (0.13), residues: 3618 helix: -0.18 (0.13), residues: 1498 sheet: 0.59 (0.19), residues: 660 loop : -1.19 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 280 HIS 0.004 0.001 HIS U 237 PHE 0.019 0.001 PHE R 691 TYR 0.021 0.001 TYR T 201 ARG 0.008 0.000 ARG X 366 *********************** 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 1017 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 888 time to evaluate : 3.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1016 LEU cc_start: 0.8117 (mm) cc_final: 0.7915 (mm) REVERT: Q 1103 ASP cc_start: 0.7620 (p0) cc_final: 0.7215 (p0) REVERT: Q 1117 ASN cc_start: 0.8425 (t0) cc_final: 0.8163 (t160) REVERT: Q 1139 GLU cc_start: 0.7229 (tp30) cc_final: 0.7003 (tp30) REVERT: Q 1167 PHE cc_start: 0.7408 (m-10) cc_final: 0.7046 (m-80) REVERT: Q 1343 ILE cc_start: 0.8332 (pt) cc_final: 0.8026 (pp) REVERT: Q 1405 MET cc_start: 0.7901 (mpp) cc_final: 0.7560 (mpp) REVERT: R 243 TYR cc_start: 0.7665 (m-10) cc_final: 0.7442 (m-10) REVERT: R 687 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7277 (mm-30) REVERT: S 80 LYS cc_start: 0.8471 (tppt) cc_final: 0.8264 (tppt) REVERT: S 154 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6961 (mm-30) REVERT: T 364 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8080 (mm) REVERT: T 431 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.8068 (mtm110) REVERT: U 62 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8400 (mt0) REVERT: V 268 MET cc_start: 0.8070 (tpp) cc_final: 0.7787 (tpp) REVERT: X 37 GLU cc_start: 0.7069 (pm20) cc_final: 0.6720 (pm20) REVERT: X 56 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7560 (mt-10) REVERT: X 94 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: X 242 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6514 (mm-30) REVERT: Y 134 GLU cc_start: 0.7443 (mp0) cc_final: 0.7240 (mp0) REVERT: Y 276 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7414 (ttpp) REVERT: Z 311 ARG cc_start: 0.7830 (mpp80) cc_final: 0.7472 (mtt-85) outliers start: 129 outliers final: 53 residues processed: 945 average time/residue: 1.5593 time to fit residues: 1690.5116 Evaluate side-chains 916 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 859 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1187 MET Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 256 ASN Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 703 SER Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 150 GLU Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 283 LYS Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 429 SER Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 438 LYS Chi-restraints excluded: chain U residue 444 GLU Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 154 ASN Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 346 ASP Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 452 SER Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 428 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 0.0770 chunk 101 optimal weight: 0.5980 chunk 272 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 328 optimal weight: 0.7980 chunk 354 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 325 optimal weight: 0.8980 chunk 111 optimal weight: 0.0070 chunk 263 optimal weight: 2.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 146 GLN R 611 GLN R 723 GLN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 441 GLN V 205 ASN V 394 GLN X 190 GLN X 256 ASN X 289 ASN X 325 ASN ** Y 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Y 443 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29098 Z= 0.178 Angle : 0.533 9.455 39368 Z= 0.263 Chirality : 0.042 0.156 4620 Planarity : 0.004 0.056 5039 Dihedral : 7.771 141.340 4006 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.08 % Allowed : 24.56 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3618 helix: 0.43 (0.14), residues: 1502 sheet: 0.69 (0.20), residues: 648 loop : -1.03 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 280 HIS 0.006 0.001 HIS V 27 PHE 0.017 0.001 PHE R 691 TYR 0.023 0.001 TYR X 323 ARG 0.007 0.000 ARG X 366 *********************** 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 1014 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 885 time to evaluate : 3.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1016 LEU cc_start: 0.8120 (mm) cc_final: 0.7860 (mm) REVERT: Q 1139 GLU cc_start: 0.7188 (tp30) cc_final: 0.6965 (tp30) REVERT: Q 1167 PHE cc_start: 0.7450 (m-10) cc_final: 0.6991 (m-80) REVERT: Q 1184 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.5616 (pp20) REVERT: Q 1321 TYR cc_start: 0.7109 (m-80) cc_final: 0.6428 (t80) REVERT: Q 1343 ILE cc_start: 0.8319 (pt) cc_final: 0.8010 (pp) REVERT: Q 1405 MET cc_start: 0.7853 (mpp) cc_final: 0.7486 (mpp) REVERT: R 152 GLN cc_start: 0.6815 (tm-30) cc_final: 0.6337 (tm-30) REVERT: R 242 GLN cc_start: 0.8115 (mt0) cc_final: 0.7523 (mt0) REVERT: R 243 TYR cc_start: 0.7704 (m-10) cc_final: 0.7483 (m-10) REVERT: R 659 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7037 (mm-40) REVERT: R 663 ASP cc_start: 0.7800 (m-30) cc_final: 0.7476 (m-30) REVERT: R 687 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7279 (mm-30) REVERT: S 80 LYS cc_start: 0.8483 (tppt) cc_final: 0.8246 (tppt) REVERT: T 364 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8090 (mm) REVERT: T 431 ARG cc_start: 0.8310 (mtm-85) cc_final: 0.8054 (mtm110) REVERT: U 62 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8425 (mt0) REVERT: U 413 ARG cc_start: 0.8297 (mtp-110) cc_final: 0.8056 (mtm-85) REVERT: W 330 SER cc_start: 0.8337 (p) cc_final: 0.8098 (m) REVERT: X 37 GLU cc_start: 0.7015 (pm20) cc_final: 0.6694 (pm20) REVERT: X 77 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7666 (pp) REVERT: X 94 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7487 (mt0) REVERT: X 203 GLU cc_start: 0.7004 (pm20) cc_final: 0.6450 (pm20) REVERT: Y 157 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7879 (mptp) REVERT: Y 276 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7231 (ttpp) REVERT: Z 311 ARG cc_start: 0.7860 (mpp80) cc_final: 0.7477 (mtt-85) outliers start: 129 outliers final: 63 residues processed: 944 average time/residue: 1.5656 time to fit residues: 1698.4646 Evaluate side-chains 931 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 861 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1035 THR Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1169 THR Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1328 MET Chi-restraints excluded: chain Q residue 1415 ARG Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 703 SER Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain T residue 184 THR Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 429 SER Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 346 ASP Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 154 ASN Chi-restraints excluded: chain V residue 190 GLN Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 385 GLU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 245 GLN Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 391 GLU Chi-restraints excluded: chain X residue 452 SER Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 432 ASP Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 0.0370 chunk 246 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 156 optimal weight: 0.0060 chunk 220 optimal weight: 0.5980 chunk 329 optimal weight: 3.9990 chunk 348 optimal weight: 0.0970 chunk 172 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.3072 ------------------------------------------------------------------------------- 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 146 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 GLN R 723 GLN T 29 HIS T 256 ASN T 289 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 441 GLN U 446 GLN V 205 ASN X 190 GLN X 256 ASN X 325 ASN Y 173 ASN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29098 Z= 0.151 Angle : 0.514 7.750 39368 Z= 0.254 Chirality : 0.042 0.142 4620 Planarity : 0.003 0.050 5039 Dihedral : 7.823 150.727 4006 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.86 % Allowed : 25.63 % Favored : 70.51 % 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: 0.10 (0.14), residues: 3618 helix: 0.76 (0.14), residues: 1499 sheet: 0.76 (0.20), residues: 645 loop : -0.92 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 280 HIS 0.006 0.001 HIS V 165 PHE 0.019 0.001 PHE R 70 TYR 0.022 0.001 TYR R 34 ARG 0.008 0.000 ARG X 366 *********************** 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 1009 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 887 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1016 LEU cc_start: 0.8160 (mm) cc_final: 0.7891 (mm) REVERT: Q 1122 TYR cc_start: 0.8709 (t80) cc_final: 0.8307 (t80) REVERT: Q 1139 GLU cc_start: 0.7166 (tp30) cc_final: 0.6953 (tp30) REVERT: Q 1167 PHE cc_start: 0.7437 (m-10) cc_final: 0.6990 (m-80) REVERT: Q 1184 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5585 (pp20) REVERT: Q 1321 TYR cc_start: 0.7123 (m-80) cc_final: 0.6429 (t80) REVERT: Q 1343 ILE cc_start: 0.8265 (pt) cc_final: 0.7934 (pp) REVERT: Q 1405 MET cc_start: 0.7855 (mpp) cc_final: 0.7516 (mpp) REVERT: R 34 TYR cc_start: 0.8146 (t80) cc_final: 0.7895 (t80) REVERT: R 152 GLN cc_start: 0.6808 (tm-30) cc_final: 0.6251 (tm-30) REVERT: R 242 GLN cc_start: 0.8114 (mt0) cc_final: 0.7491 (mt0) REVERT: R 664 MET cc_start: 0.8515 (mtp) cc_final: 0.8218 (ttm) REVERT: R 687 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7252 (mm-30) REVERT: R 736 GLU cc_start: 0.7471 (tt0) cc_final: 0.7201 (tt0) REVERT: S 80 LYS cc_start: 0.8481 (tppt) cc_final: 0.8238 (tppt) REVERT: T 359 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8317 (m) REVERT: T 364 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8098 (mm) REVERT: T 431 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.8018 (mtm180) REVERT: U 62 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8422 (mt0) REVERT: U 66 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8368 (mt) REVERT: W 208 ARG cc_start: 0.5768 (OUTLIER) cc_final: 0.4810 (tpt-90) REVERT: W 330 SER cc_start: 0.8299 (p) cc_final: 0.8090 (m) REVERT: X 37 GLU cc_start: 0.7014 (pm20) cc_final: 0.6699 (pm20) REVERT: X 77 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7631 (pp) REVERT: X 94 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7445 (mt0) REVERT: X 203 GLU cc_start: 0.6921 (pm20) cc_final: 0.6297 (pm20) REVERT: X 240 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7571 (mtmt) REVERT: Y 157 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7799 (mptp) REVERT: Y 276 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7059 (ttpp) REVERT: Z 311 ARG cc_start: 0.7856 (mpp80) cc_final: 0.7506 (mtt-85) outliers start: 122 outliers final: 59 residues processed: 942 average time/residue: 1.5964 time to fit residues: 1726.9430 Evaluate side-chains 945 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 876 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1415 ARG Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 278 GLU Chi-restraints excluded: chain R residue 703 SER Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 283 LYS Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 359 VAL Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 346 ASP Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain V residue 385 GLU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 182 ASP Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 245 GLN Chi-restraints excluded: chain X residue 246 ASP Chi-restraints excluded: chain X residue 319 GLU Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 391 GLU Chi-restraints excluded: chain X residue 452 SER Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 432 ASP Chi-restraints excluded: chain Y residue 456 ILE 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: 0.3980 chunk 5 optimal weight: 0.3980 chunk 259 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 297 optimal weight: 0.9990 chunk 241 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 313 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1207 GLN R 144 GLN R 146 GLN R 224 ASN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 GLN T 256 ASN T 289 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 441 GLN U 446 GLN V 205 ASN V 394 GLN X 190 GLN X 256 ASN X 289 ASN X 325 ASN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 441 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29098 Z= 0.232 Angle : 0.553 11.290 39368 Z= 0.273 Chirality : 0.043 0.217 4620 Planarity : 0.003 0.048 5039 Dihedral : 7.898 152.258 4006 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.30 % Allowed : 25.73 % Favored : 69.97 % 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: 0.15 (0.14), residues: 3618 helix: 0.78 (0.14), residues: 1505 sheet: 0.73 (0.20), residues: 664 loop : -0.87 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 280 HIS 0.006 0.001 HIS V 165 PHE 0.016 0.001 PHE R 691 TYR 0.022 0.002 TYR V 201 ARG 0.010 0.000 ARG X 366 *********************** 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 1014 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 878 time to evaluate : 3.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 1016 LEU cc_start: 0.8212 (mm) cc_final: 0.7930 (mm) REVERT: Q 1117 ASN cc_start: 0.8387 (t0) cc_final: 0.8092 (t160) REVERT: Q 1139 GLU cc_start: 0.7187 (tp30) cc_final: 0.6981 (tp30) REVERT: Q 1167 PHE cc_start: 0.7588 (m-10) cc_final: 0.7183 (m-80) REVERT: Q 1184 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5643 (pp20) REVERT: Q 1321 TYR cc_start: 0.7178 (m-80) cc_final: 0.6444 (t80) REVERT: Q 1343 ILE cc_start: 0.8200 (pt) cc_final: 0.7846 (pp) REVERT: Q 1405 MET cc_start: 0.7923 (mpp) cc_final: 0.7540 (mpp) REVERT: R 74 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8101 (tmmt) REVERT: R 152 GLN cc_start: 0.6878 (tm-30) cc_final: 0.6340 (tm-30) REVERT: R 242 GLN cc_start: 0.8087 (mt0) cc_final: 0.7380 (mt0) REVERT: R 263 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8376 (ptmm) REVERT: R 659 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7361 (mm-40) REVERT: R 687 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7297 (mm-30) REVERT: R 736 GLU cc_start: 0.7477 (tt0) cc_final: 0.7199 (tt0) REVERT: T 359 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8370 (m) REVERT: T 364 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8149 (mm) REVERT: U 62 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8468 (mt0) REVERT: V 319 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: V 341 ASN cc_start: 0.8419 (p0) cc_final: 0.8103 (p0) REVERT: W 208 ARG cc_start: 0.5760 (OUTLIER) cc_final: 0.4797 (tpt-90) REVERT: X 35 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8602 (mt) REVERT: X 37 GLU cc_start: 0.7024 (pm20) cc_final: 0.6708 (pm20) REVERT: X 77 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7661 (pp) REVERT: X 94 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7461 (mt0) REVERT: X 99 LYS cc_start: 0.7790 (mmtt) cc_final: 0.7469 (mmtt) REVERT: X 203 GLU cc_start: 0.6977 (pm20) cc_final: 0.6258 (pm20) REVERT: Y 157 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7879 (mptp) REVERT: Y 276 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7420 (ttpp) REVERT: Y 297 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: Z 311 ARG cc_start: 0.7876 (mpp80) cc_final: 0.7523 (mtt-85) outliers start: 136 outliers final: 75 residues processed: 933 average time/residue: 1.5908 time to fit residues: 1705.0927 Evaluate side-chains 942 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 853 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1169 THR Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1187 MET Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1415 ARG Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 703 SER Chi-restraints excluded: chain R residue 723 GLN Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain R residue 750 THR Chi-restraints excluded: chain S residue 49 LYS Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 184 THR Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 282 GLU Chi-restraints excluded: chain T residue 283 LYS Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 359 VAL Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 429 SER Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 346 ASP Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 154 ASN Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain X residue 35 LEU Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 182 ASP Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 245 GLN Chi-restraints excluded: chain X residue 246 ASP Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 391 GLU Chi-restraints excluded: chain X residue 452 SER Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 193 ASP Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 229 LEU Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 297 GLU Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 432 ASP Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 0.6980 chunk 314 optimal weight: 4.9990 chunk 68 optimal weight: 0.2980 chunk 204 optimal weight: 0.0970 chunk 86 optimal weight: 0.2980 chunk 349 optimal weight: 0.8980 chunk 289 optimal weight: 0.5980 chunk 161 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1207 GLN ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 GLN T 256 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 441 GLN U 446 GLN V 205 ASN X 190 GLN X 256 ASN X 289 ASN X 325 ASN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 441 GLN Y 443 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29098 Z= 0.164 Angle : 0.523 8.537 39368 Z= 0.258 Chirality : 0.042 0.157 4620 Planarity : 0.003 0.046 5039 Dihedral : 7.677 152.278 4006 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.96 % Allowed : 26.49 % Favored : 69.56 % 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: 0.29 (0.14), residues: 3618 helix: 0.93 (0.14), residues: 1503 sheet: 0.76 (0.20), residues: 664 loop : -0.80 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 280 HIS 0.004 0.001 HIS V 165 PHE 0.018 0.001 PHE R 691 TYR 0.024 0.001 TYR R 34 ARG 0.009 0.000 ARG X 366 *********************** 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 1005 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 880 time to evaluate : 3.579 Fit side-chains revert: symmetry clash REVERT: Q 1016 LEU cc_start: 0.8191 (mm) cc_final: 0.7912 (mm) REVERT: Q 1122 TYR cc_start: 0.8708 (t80) cc_final: 0.8293 (t80) REVERT: Q 1167 PHE cc_start: 0.7502 (m-10) cc_final: 0.6975 (m-80) REVERT: Q 1184 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.5627 (pp20) REVERT: Q 1204 ASN cc_start: 0.8102 (p0) cc_final: 0.7771 (p0) REVERT: Q 1321 TYR cc_start: 0.7181 (m-80) cc_final: 0.6479 (t80) REVERT: Q 1327 MET cc_start: 0.4541 (mmm) cc_final: 0.4106 (tmm) REVERT: Q 1343 ILE cc_start: 0.8176 (pt) cc_final: 0.7829 (pp) REVERT: Q 1405 MET cc_start: 0.7915 (mpp) cc_final: 0.7617 (mtm) REVERT: R 152 GLN cc_start: 0.6864 (tm-30) cc_final: 0.6301 (tm-30) REVERT: R 227 MET cc_start: 0.8545 (mmp) cc_final: 0.8127 (mmt) REVERT: R 242 GLN cc_start: 0.8040 (mt0) cc_final: 0.7314 (mt0) REVERT: R 263 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8376 (ptmm) REVERT: R 659 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7439 (mm-40) REVERT: R 664 MET cc_start: 0.8504 (mtp) cc_final: 0.8192 (ttm) REVERT: R 687 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7331 (mm-30) REVERT: R 736 GLU cc_start: 0.7467 (tt0) cc_final: 0.7186 (tt0) REVERT: T 359 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8338 (m) REVERT: T 364 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8125 (mm) REVERT: T 431 ARG cc_start: 0.8312 (mtm-85) cc_final: 0.7925 (mtm180) REVERT: U 62 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8448 (mt0) REVERT: V 319 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7417 (mm-30) REVERT: V 341 ASN cc_start: 0.8398 (p0) cc_final: 0.8097 (p0) REVERT: W 208 ARG cc_start: 0.5737 (OUTLIER) cc_final: 0.4784 (tpt-90) REVERT: X 35 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8575 (mt) REVERT: X 37 GLU cc_start: 0.6982 (pm20) cc_final: 0.6657 (pm20) REVERT: X 77 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7643 (pp) REVERT: X 94 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7412 (mt0) REVERT: X 99 LYS cc_start: 0.7793 (mmtt) cc_final: 0.7483 (mmtt) REVERT: X 203 GLU cc_start: 0.6999 (pm20) cc_final: 0.6318 (pm20) REVERT: X 344 MET cc_start: 0.8902 (mmt) cc_final: 0.8565 (mmt) REVERT: Y 157 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7655 (mtpt) REVERT: Y 276 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.6943 (ttpp) REVERT: Z 311 ARG cc_start: 0.7855 (mpp80) cc_final: 0.7513 (mtt-85) outliers start: 125 outliers final: 70 residues processed: 932 average time/residue: 1.5988 time to fit residues: 1707.0251 Evaluate side-chains 938 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 856 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1161 ASN Chi-restraints excluded: chain Q residue 1169 THR Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1415 ARG Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 703 SER Chi-restraints excluded: chain R residue 723 GLN Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain S residue 49 LYS Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 150 GLU Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 167 ILE Chi-restraints excluded: chain T residue 184 THR Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 283 LYS Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 359 VAL Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 346 ASP Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain V residue 154 ASN Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 285 LYS Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain X residue 35 LEU Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 240 LYS Chi-restraints excluded: chain X residue 245 GLN Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 391 GLU Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 454 LYS Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 229 LEU Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 432 ASP Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 chunk 199 optimal weight: 0.6980 chunk 255 optimal weight: 0.0270 chunk 197 optimal weight: 0.9980 chunk 294 optimal weight: 0.3980 chunk 195 optimal weight: 0.8980 chunk 347 optimal weight: 0.0020 chunk 217 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 overall best weight: 0.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 146 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 GLN S 40 ASN T 256 ASN T 289 ASN T 325 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 446 GLN V 205 ASN V 314 ASN X 190 GLN X 256 ASN X 289 ASN Y 47 GLN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 441 GLN Y 446 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29098 Z= 0.131 Angle : 0.508 9.678 39368 Z= 0.250 Chirality : 0.041 0.163 4620 Planarity : 0.003 0.044 5039 Dihedral : 7.362 146.093 4006 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.35 % Allowed : 27.28 % Favored : 69.37 % 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: 0.42 (0.14), residues: 3618 helix: 1.07 (0.14), residues: 1500 sheet: 0.78 (0.19), residues: 691 loop : -0.77 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 280 HIS 0.004 0.001 HIS V 165 PHE 0.017 0.001 PHE R 691 TYR 0.026 0.001 TYR R 34 ARG 0.010 0.000 ARG X 366 *********************** 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 972 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 866 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1117 ASN cc_start: 0.8219 (t0) cc_final: 0.8004 (t160) REVERT: Q 1122 TYR cc_start: 0.8694 (t80) cc_final: 0.8281 (t80) REVERT: Q 1184 GLU cc_start: 0.5946 (OUTLIER) cc_final: 0.5622 (pp20) REVERT: Q 1321 TYR cc_start: 0.7192 (m-80) cc_final: 0.6489 (t80) REVERT: Q 1343 ILE cc_start: 0.8147 (pt) cc_final: 0.7816 (pp) REVERT: Q 1405 MET cc_start: 0.7985 (mpp) cc_final: 0.7746 (mpp) REVERT: R 242 GLN cc_start: 0.8003 (mt0) cc_final: 0.7273 (mt0) REVERT: R 263 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8371 (ptmm) REVERT: R 659 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7453 (mm-40) REVERT: R 687 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7265 (mm-30) REVERT: R 724 TYR cc_start: 0.7195 (t80) cc_final: 0.6700 (t80) REVERT: R 736 GLU cc_start: 0.7460 (tt0) cc_final: 0.7215 (tt0) REVERT: T 364 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8083 (mm) REVERT: T 431 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.7922 (mtm110) REVERT: U 62 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8446 (mt0) REVERT: V 341 ASN cc_start: 0.8363 (p0) cc_final: 0.8099 (p0) REVERT: V 373 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8661 (mp) REVERT: W 139 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: W 208 ARG cc_start: 0.5684 (OUTLIER) cc_final: 0.4766 (tpt-90) REVERT: X 35 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8572 (mt) REVERT: X 37 GLU cc_start: 0.6976 (pm20) cc_final: 0.6650 (pm20) REVERT: X 77 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7594 (pp) REVERT: X 94 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7405 (mt0) REVERT: X 99 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7532 (mmtt) REVERT: X 203 GLU cc_start: 0.7000 (pm20) cc_final: 0.6359 (pm20) REVERT: X 344 MET cc_start: 0.8881 (mmt) cc_final: 0.8547 (mmt) REVERT: Y 157 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7592 (mtpt) REVERT: Y 276 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7689 (tttp) REVERT: Z 311 ARG cc_start: 0.7842 (mpp80) cc_final: 0.7500 (mtt-85) outliers start: 106 outliers final: 62 residues processed: 913 average time/residue: 1.5787 time to fit residues: 1654.3923 Evaluate side-chains 928 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 854 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 278 GLU Chi-restraints excluded: chain R residue 591 LEU Chi-restraints excluded: chain R residue 703 SER Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain S residue 49 LYS Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 150 GLU Chi-restraints excluded: chain T residue 181 LEU Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 402 LEU Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 154 ASN Chi-restraints excluded: chain V residue 171 LYS Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain V residue 385 GLU Chi-restraints excluded: chain W residue 139 GLU Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 285 LYS Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain X residue 35 LEU Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 391 GLU Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 452 SER Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 432 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 273 optimal weight: 0.0670 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1097 ASN ** Q1204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1207 GLN R 146 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 GLN T 205 ASN T 256 ASN T 289 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 446 GLN V 205 ASN V 314 ASN X 190 GLN X 256 ASN X 289 ASN X 325 ASN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 441 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 29098 Z= 0.304 Angle : 0.597 10.716 39368 Z= 0.296 Chirality : 0.045 0.180 4620 Planarity : 0.004 0.058 5039 Dihedral : 7.717 148.001 4004 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.02 % Allowed : 27.12 % Favored : 68.86 % 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: 0.86 (0.14), residues: 1502 sheet: 0.77 (0.20), residues: 669 loop : -0.83 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 280 HIS 0.006 0.001 HIS V 165 PHE 0.023 0.002 PHE Q1167 TYR 0.033 0.002 TYR X 323 ARG 0.009 0.000 ARG T 132 *********************** 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 1018 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 891 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 1122 TYR cc_start: 0.8746 (t80) cc_final: 0.8286 (t80) REVERT: Q 1167 PHE cc_start: 0.7370 (m-80) cc_final: 0.7010 (m-80) REVERT: Q 1184 GLU cc_start: 0.6003 (OUTLIER) cc_final: 0.5676 (pp20) REVERT: Q 1321 TYR cc_start: 0.7181 (m-80) cc_final: 0.6437 (t80) REVERT: Q 1327 MET cc_start: 0.4445 (mmm) cc_final: 0.4157 (tmm) REVERT: Q 1343 ILE cc_start: 0.8130 (pt) cc_final: 0.7781 (pp) REVERT: Q 1405 MET cc_start: 0.8027 (mpp) cc_final: 0.7641 (mtm) REVERT: R 90 GLN cc_start: 0.7399 (tp-100) cc_final: 0.7076 (tp-100) REVERT: R 152 GLN cc_start: 0.6922 (tm-30) cc_final: 0.6370 (tm-30) REVERT: R 242 GLN cc_start: 0.8048 (mt0) cc_final: 0.7285 (mt0) REVERT: R 263 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8380 (ptmm) REVERT: R 659 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7459 (mm-40) REVERT: R 687 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7295 (mm-30) REVERT: R 736 GLU cc_start: 0.7485 (tt0) cc_final: 0.7177 (tt0) REVERT: T 364 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8139 (mm) REVERT: T 431 ARG cc_start: 0.8318 (mtm-85) cc_final: 0.7966 (mtm110) REVERT: T 456 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8283 (mp) REVERT: V 205 ASN cc_start: 0.8525 (m110) cc_final: 0.8275 (m-40) REVERT: V 227 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7081 (mm-30) REVERT: V 319 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7423 (mm-30) REVERT: V 341 ASN cc_start: 0.8483 (p0) cc_final: 0.8126 (p0) REVERT: V 433 GLU cc_start: 0.7227 (tp30) cc_final: 0.6918 (mm-30) REVERT: W 208 ARG cc_start: 0.5683 (OUTLIER) cc_final: 0.4775 (tpt-90) REVERT: X 37 GLU cc_start: 0.7029 (pm20) cc_final: 0.6713 (pm20) REVERT: X 77 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7593 (pp) REVERT: X 94 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7486 (mt0) REVERT: X 99 LYS cc_start: 0.7830 (mmtt) cc_final: 0.7549 (mmtt) REVERT: X 203 GLU cc_start: 0.7021 (pm20) cc_final: 0.6343 (pm20) REVERT: X 344 MET cc_start: 0.8866 (mmt) cc_final: 0.8552 (mmt) REVERT: Y 157 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7874 (mtpt) REVERT: Y 276 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7615 (ttpp) REVERT: Y 297 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: Z 311 ARG cc_start: 0.7860 (mpp80) cc_final: 0.7517 (mtt-85) outliers start: 127 outliers final: 72 residues processed: 949 average time/residue: 1.6015 time to fit residues: 1750.6100 Evaluate side-chains 960 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 877 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1161 ASN Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1371 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 703 SER Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain S residue 49 LYS Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 150 GLU Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 184 THR Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 282 GLU Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 402 LEU Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain T residue 429 SER Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain T residue 456 LEU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 346 ASP Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 154 ASN Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain W residue 139 GLU Chi-restraints excluded: chain W residue 174 LYS Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 198 ASP Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 246 ASP Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 452 SER Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 158 LEU Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 193 ASP Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 297 GLU Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 378 GLU Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 432 ASP Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 0.9980 chunk 333 optimal weight: 1.9990 chunk 304 optimal weight: 0.1980 chunk 324 optimal weight: 0.7980 chunk 195 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 254 optimal weight: 0.9990 chunk 99 optimal weight: 0.0070 chunk 292 optimal weight: 0.5980 chunk 306 optimal weight: 0.1980 chunk 323 optimal weight: 0.0030 overall best weight: 0.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 146 GLN R 611 GLN R 723 GLN T 256 ASN U 62 GLN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 446 GLN W 310 ASN W 443 ASN X 190 GLN X 245 GLN X 256 ASN X 289 ASN X 325 ASN Y 23 HIS Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Y 443 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29098 Z= 0.139 Angle : 0.529 9.631 39368 Z= 0.260 Chirality : 0.042 0.188 4620 Planarity : 0.003 0.053 5039 Dihedral : 7.305 142.835 4004 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.63 % Allowed : 28.77 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3618 helix: 1.01 (0.14), residues: 1503 sheet: 0.76 (0.19), residues: 702 loop : -0.75 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Y 280 HIS 0.004 0.001 HIS V 165 PHE 0.032 0.001 PHE Q1167 TYR 0.026 0.001 TYR R 34 ARG 0.008 0.000 ARG W 327 *********************** 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 962 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 879 time to evaluate : 3.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 1122 TYR cc_start: 0.8709 (t80) cc_final: 0.8292 (t80) REVERT: Q 1184 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.5633 (pp20) REVERT: Q 1321 TYR cc_start: 0.7125 (m-80) cc_final: 0.6410 (t80) REVERT: Q 1343 ILE cc_start: 0.8135 (pt) cc_final: 0.7792 (pp) REVERT: Q 1405 MET cc_start: 0.7995 (mpp) cc_final: 0.7601 (mtm) REVERT: R 90 GLN cc_start: 0.7351 (tp-100) cc_final: 0.7031 (tp-100) REVERT: R 152 GLN cc_start: 0.6865 (tm-30) cc_final: 0.6288 (tm-30) REVERT: R 242 GLN cc_start: 0.7979 (mt0) cc_final: 0.7241 (mt0) REVERT: R 263 LYS cc_start: 0.8649 (ptmm) cc_final: 0.8378 (ptmm) REVERT: R 659 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7514 (mm-40) REVERT: R 687 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7218 (mm-30) REVERT: R 736 GLU cc_start: 0.7456 (tt0) cc_final: 0.7159 (tt0) REVERT: T 431 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.7911 (mtm110) REVERT: U 230 GLN cc_start: 0.8480 (tt0) cc_final: 0.8227 (tt0) REVERT: U 450 ASP cc_start: 0.7917 (m-30) cc_final: 0.7705 (m-30) REVERT: V 319 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7419 (mm-30) REVERT: V 341 ASN cc_start: 0.8411 (p0) cc_final: 0.8125 (p0) REVERT: V 433 GLU cc_start: 0.7218 (tp30) cc_final: 0.6933 (tm-30) REVERT: W 208 ARG cc_start: 0.5659 (OUTLIER) cc_final: 0.4748 (tpt-90) REVERT: W 297 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7789 (mt-10) REVERT: X 37 GLU cc_start: 0.6989 (pm20) cc_final: 0.6671 (pm20) REVERT: X 77 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7597 (pp) REVERT: X 94 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7401 (mt0) REVERT: X 99 LYS cc_start: 0.7817 (mmtt) cc_final: 0.7531 (mmtt) REVERT: X 203 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6300 (pm20) REVERT: Y 23 HIS cc_start: 0.8496 (OUTLIER) cc_final: 0.7232 (p-80) REVERT: Y 157 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7519 (mtpt) REVERT: Y 276 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7903 (ttpp) REVERT: Z 311 ARG cc_start: 0.7808 (mpp80) cc_final: 0.7390 (mtt180) outliers start: 83 outliers final: 49 residues processed: 918 average time/residue: 1.6564 time to fit residues: 1768.4840 Evaluate side-chains 926 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 868 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1071 THR Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1161 ASN Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1371 LEU Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 278 GLU Chi-restraints excluded: chain R residue 591 LEU Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain S residue 49 LYS Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 150 GLU Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 181 LEU Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 424 LYS Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 154 ASN Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 198 ASP Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 203 GLU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 365 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 391 GLU Chi-restraints excluded: chain X residue 452 SER Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 432 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 0.9990 chunk 342 optimal weight: 0.2980 chunk 209 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 chunk 359 optimal weight: 0.4980 chunk 331 optimal weight: 0.0070 chunk 286 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 175 optimal weight: 0.0870 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1097 ASN Q1117 ASN Q1207 GLN R 146 GLN R 611 GLN T 256 ASN T 289 ASN ** T 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN V 205 ASN W 310 ASN W 443 ASN X 190 GLN X 256 ASN X 325 ASN Y 23 HIS Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Y 446 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29098 Z= 0.167 Angle : 0.548 11.802 39368 Z= 0.269 Chirality : 0.043 0.270 4620 Planarity : 0.003 0.050 5039 Dihedral : 7.263 142.596 4004 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.18 % Allowed : 29.49 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3618 helix: 1.04 (0.14), residues: 1498 sheet: 0.77 (0.19), residues: 712 loop : -0.72 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 280 HIS 0.006 0.001 HIS Y 25 PHE 0.024 0.001 PHE Q1167 TYR 0.028 0.001 TYR R 34 ARG 0.009 0.000 ARG S 73 ********************** 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 944 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 875 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 1122 TYR cc_start: 0.8718 (t80) cc_final: 0.8240 (t80) REVERT: Q 1184 GLU cc_start: 0.5971 (OUTLIER) cc_final: 0.5657 (pp20) REVERT: Q 1321 TYR cc_start: 0.7146 (m-80) cc_final: 0.6430 (t80) REVERT: Q 1327 MET cc_start: 0.4273 (mmm) cc_final: 0.3922 (tmm) REVERT: Q 1343 ILE cc_start: 0.8128 (pt) cc_final: 0.7784 (pp) REVERT: Q 1405 MET cc_start: 0.7997 (mpp) cc_final: 0.7582 (mtm) REVERT: R 90 GLN cc_start: 0.7344 (tp-100) cc_final: 0.7031 (tp-100) REVERT: R 152 GLN cc_start: 0.6875 (tm-30) cc_final: 0.6304 (tm-30) REVERT: R 242 GLN cc_start: 0.7967 (mt0) cc_final: 0.7216 (mt0) REVERT: R 263 LYS cc_start: 0.8634 (ptmm) cc_final: 0.8360 (ptmm) REVERT: R 687 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7225 (mm-30) REVERT: R 736 GLU cc_start: 0.7463 (tt0) cc_final: 0.7168 (tt0) REVERT: T 431 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7903 (mtm110) REVERT: U 450 ASP cc_start: 0.7937 (m-30) cc_final: 0.7693 (m-30) REVERT: V 341 ASN cc_start: 0.8406 (p0) cc_final: 0.8137 (p0) REVERT: V 433 GLU cc_start: 0.7224 (tp30) cc_final: 0.6950 (tm-30) REVERT: W 208 ARG cc_start: 0.5642 (OUTLIER) cc_final: 0.4733 (tpt-90) REVERT: W 297 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7807 (mt-10) REVERT: X 37 GLU cc_start: 0.7002 (pm20) cc_final: 0.6685 (pm20) REVERT: X 77 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7582 (pp) REVERT: X 94 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: X 99 LYS cc_start: 0.7829 (mmtt) cc_final: 0.7534 (mmtt) REVERT: X 203 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6288 (pm20) REVERT: Y 23 HIS cc_start: 0.8516 (OUTLIER) cc_final: 0.7163 (p-80) REVERT: Y 157 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7688 (mtpt) REVERT: Y 276 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7926 (ttpp) REVERT: Z 311 ARG cc_start: 0.7860 (mpp80) cc_final: 0.7463 (mtt180) outliers start: 69 outliers final: 51 residues processed: 903 average time/residue: 1.5669 time to fit residues: 1625.2496 Evaluate side-chains 928 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 869 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1071 THR Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1161 ASN Chi-restraints excluded: chain Q residue 1169 THR Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1371 LEU Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 591 LEU Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain S residue 49 LYS Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 150 GLU Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 424 LYS Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 154 ASN Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 198 ASP Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 203 GLU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 246 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 391 GLU Chi-restraints excluded: chain X residue 452 SER Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 432 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 4.9990 chunk 305 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 286 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 294 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1117 ASN ** Q1204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1207 GLN R 146 GLN R 177 ASN R 611 GLN T 205 ASN T 256 ASN T 289 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 446 GLN V 205 ASN W 310 ASN W 443 ASN X 190 GLN X 256 ASN X 289 ASN X 325 ASN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109329 restraints weight = 39482.995| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.96 r_work: 0.3323 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 29098 Z= 0.313 Angle : 0.619 11.157 39368 Z= 0.306 Chirality : 0.046 0.259 4620 Planarity : 0.004 0.077 5039 Dihedral : 7.639 145.146 4004 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.63 % Allowed : 29.18 % Favored : 68.20 % 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: 0.18 (0.14), residues: 3618 helix: 0.78 (0.14), residues: 1512 sheet: 0.74 (0.20), residues: 678 loop : -0.83 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Y 280 HIS 0.018 0.001 HIS Y 23 PHE 0.030 0.002 PHE Q1167 TYR 0.038 0.002 TYR X 323 ARG 0.011 0.001 ARG S 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20960.38 seconds wall clock time: 368 minutes 54.23 seconds (22134.23 seconds total)