Starting phenix.real_space_refine on Wed Mar 20 22:43:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etu_28599/03_2024/8etu_28599_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etu_28599/03_2024/8etu_28599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etu_28599/03_2024/8etu_28599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etu_28599/03_2024/8etu_28599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etu_28599/03_2024/8etu_28599_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etu_28599/03_2024/8etu_28599_updated.pdb" } resolution = 2.8 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 95 5.16 5 C 18041 2.51 5 N 4942 2.21 5 O 5580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 192": "OE1" <-> "OE2" Residue "R TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 259": "OE1" <-> "OE2" Residue "R GLU 268": "OE1" <-> "OE2" Residue "R TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "S ASP 69": "OD1" <-> "OD2" Residue "T GLU 141": "OE1" <-> "OE2" Residue "T ASP 151": "OD1" <-> "OD2" Residue "T TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 351": "OE1" <-> "OE2" Residue "U GLU 33": "OE1" <-> "OE2" Residue "U ASP 95": "OD1" <-> "OD2" Residue "U GLU 110": "OE1" <-> "OE2" Residue "U GLU 134": "OE1" <-> "OE2" Residue "U GLU 226": "OE1" <-> "OE2" Residue "U ASP 261": "OD1" <-> "OD2" Residue "U ASP 271": "OD1" <-> "OD2" Residue "U GLU 279": "OE1" <-> "OE2" Residue "U GLU 282": "OE1" <-> "OE2" Residue "U ASP 315": "OD1" <-> "OD2" Residue "U GLU 316": "OE1" <-> "OE2" Residue "U TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 376": "OE1" <-> "OE2" Residue "U GLU 378": "OE1" <-> "OE2" Residue "U GLU 421": "OE1" <-> "OE2" Residue "U TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 449": "OD1" <-> "OD2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "V GLU 153": "OE1" <-> "OE2" Residue "V ASP 182": "OD1" <-> "OD2" Residue "V GLU 192": "OE1" <-> "OE2" Residue "V TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 228": "OE1" <-> "OE2" Residue "V ASP 253": "OD1" <-> "OD2" Residue "V GLU 302": "OE1" <-> "OE2" Residue "V GLU 441": "OE1" <-> "OE2" Residue "W ASP 218": "OD1" <-> "OD2" Residue "W GLU 226": "OE1" <-> "OE2" Residue "W GLU 228": "OE1" <-> "OE2" Residue "W ASP 302": "OD1" <-> "OD2" Residue "W GLU 374": "OE1" <-> "OE2" Residue "W ASP 382": "OD1" <-> "OD2" Residue "W GLU 393": "OE1" <-> "OE2" Residue "X GLU 37": "OE1" <-> "OE2" Residue "X TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 119": "OE1" <-> "OE2" Residue "X GLU 123": "OE1" <-> "OE2" Residue "X PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 153": "OE1" <-> "OE2" Residue "X TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 227": "OE1" <-> "OE2" Residue "X TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 253": "OD1" <-> "OD2" Residue "X ASP 264": "OD1" <-> "OD2" Residue "X GLU 279": "OE1" <-> "OE2" Residue "X GLU 312": "OE1" <-> "OE2" Residue "X GLU 391": "OE1" <-> "OE2" Residue "Y GLU 33": "OE1" <-> "OE2" Residue "Y GLU 110": "OE1" <-> "OE2" Residue "Y GLU 115": "OE1" <-> "OE2" Residue "Y GLU 182": "OE1" <-> "OE2" Residue "Y ASP 213": "OD1" <-> "OD2" Residue "Y GLU 243": "OE1" <-> "OE2" Residue "Y ASP 261": "OD1" <-> "OD2" Residue "Y GLU 268": "OE1" <-> "OE2" Residue "Y GLU 282": "OE1" <-> "OE2" Residue "Y ASP 302": "OD1" <-> "OD2" Residue "Y PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 346": "OD1" <-> "OD2" Residue "Y GLU 375": "OE1" <-> "OE2" Residue "Y TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 449": "OD1" <-> "OD2" Residue "Q TYR 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 1101": "OD1" <-> "OD2" Residue "Q GLU 1173": "OE1" <-> "OE2" Residue "Q TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 1222": "OE1" <-> "OE2" Residue "Q GLU 1276": "OE1" <-> "OE2" Residue "Q ASP 1305": "OD1" <-> "OD2" Residue "Q PHE 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 1329": "OD1" <-> "OD2" Residue "Q GLU 1333": "OE1" <-> "OE2" Residue "Q ASP 1406": "OD1" <-> "OD2" Residue "Z PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 314": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28670 Number of models: 1 Model: "" Number of chains: 16 Chain: "R" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3548 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain breaks: 1 Chain: "S" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1014 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 9, 'TRANS': 115} Chain breaks: 1 Chain: "T" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3339 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3354 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3404 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "W" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3398 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 431} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "Y" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3421 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 434} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "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: "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: 14.09, per 1000 atoms: 0.49 Number of scatterers: 28670 At special positions: 0 Unit cell: (132.765, 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 5580 8.00 N 4942 7.00 C 18041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.22 Conformation dependent library (CDL) restraints added in 4.9 seconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6820 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 152 helices and 30 sheets defined 38.3% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.23 Creating SS restraints... 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 removed outlier: 4.059A pdb=" N GLU R 156 " --> pdb=" O GLN R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 176 Processing helix chain 'R' and resid 216 through 230 Processing helix chain 'R' and resid 240 through 249 Processing helix chain 'R' and resid 257 through 263 removed outlier: 3.873A pdb=" N GLU R 262 " --> pdb=" O ASP R 258 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS R 263 " --> pdb=" O GLU R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 586 through 588 No H-bonds generated for 'chain 'R' and resid 586 through 588' Processing helix chain 'R' and resid 590 through 596 Processing helix chain 'R' and resid 608 through 610 No H-bonds generated for 'chain 'R' and resid 608 through 610' Processing helix chain 'R' and resid 617 through 620 No H-bonds generated for 'chain 'R' and resid 617 through 620' Processing helix chain 'R' and resid 622 through 625 removed outlier: 3.921A pdb=" N ILE R 625 " --> pdb=" O PRO R 622 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 622 through 625' Processing helix chain 'R' and resid 628 through 630 No H-bonds generated for 'chain 'R' and resid 628 through 630' Processing helix chain 'R' and resid 638 through 648 Processing helix chain 'R' and resid 659 through 667 removed outlier: 3.544A 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 32 through 39 Processing helix chain 'S' and resid 63 through 82 removed outlier: 4.073A pdb=" N ILE S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 143 Processing helix chain 'S' and resid 152 through 158 removed outlier: 3.965A pdb=" N LEU S 158 " --> pdb=" O GLU S 154 " (cutoff:3.500A) 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: 3.676A pdb=" N LEU T 110 " --> pdb=" O GLY T 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 107 through 110' Processing helix chain 'T' and resid 117 through 128 removed outlier: 4.049A pdb=" N ALA T 128 " --> pdb=" O ASN T 124 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 192 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 329 removed outlier: 3.763A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU T 329 " --> pdb=" O ASN T 325 " (cutoff:3.500A) Processing helix chain 'T' and resid 356 through 358 No H-bonds generated for 'chain 'T' and resid 356 through 358' Processing helix chain 'T' and resid 361 through 366 removed outlier: 3.755A pdb=" N ASP T 365 " --> pdb=" O PRO T 361 " (cutoff:3.500A) removed outlier: 4.814A 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: 3.569A pdb=" N LEU T 416 " --> pdb=" O LEU T 412 " (cutoff:3.500A) removed outlier: 4.635A 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: 3.938A pdb=" N SER U 124 " --> pdb=" O ALA U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 180 Processing helix chain 'U' and resid 241 through 248 Processing helix chain 'U' and resid 254 through 259 removed outlier: 3.989A 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 314 removed outlier: 3.582A pdb=" N ARG U 311 " --> pdb=" O SER U 307 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU U 313 " --> pdb=" O ILE U 309 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU U 314 " --> pdb=" O ASN U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 340 through 342 No H-bonds generated for 'chain 'U' and resid 340 through 342' Processing helix chain 'U' and resid 345 through 350 removed outlier: 4.096A pdb=" N ARG U 350 " --> pdb=" O ASP U 346 " (cutoff:3.500A) Processing helix chain 'U' and resid 361 through 374 Processing helix chain 'U' and resid 381 through 393 Processing helix chain 'U' and resid 396 through 412 removed outlier: 4.583A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE U 409 " --> pdb=" O VAL U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 420 through 429 Processing helix chain 'U' and resid 433 through 441 Processing helix chain 'V' and resid 52 through 67 Processing helix chain 'V' and resid 86 through 96 Processing helix chain 'V' and resid 107 through 110 removed outlier: 3.877A 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: 3.691A 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 272 removed outlier: 3.548A pdb=" N GLN V 271 " --> pdb=" O SER V 267 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU V 272 " --> pdb=" O MET V 268 " (cutoff:3.500A) 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: 3.727A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) removed outlier: 4.325A 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: 3.705A pdb=" N ASP V 365 " --> pdb=" O PRO V 361 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG V 366 " --> pdb=" O ASP V 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 361 through 366' 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 417 Processing helix chain 'V' and resid 419 through 429 removed outlier: 3.705A 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 103 through 105 No H-bonds generated for 'chain 'W' and resid 103 through 105' Processing helix chain 'W' and resid 113 through 124 removed outlier: 4.028A 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: 4.048A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 267 through 283 Processing helix chain 'W' and resid 303 through 314 removed outlier: 3.865A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) removed outlier: 4.737A 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: 3.924A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS W 412 " --> pdb=" O GLN W 408 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 429 Processing helix chain 'W' and resid 433 through 441 Processing helix chain 'X' and resid 52 through 67 Processing helix chain 'X' and resid 85 through 96 Processing helix chain 'X' and resid 107 through 110 removed outlier: 4.011A 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: 3.938A pdb=" N ALA X 128 " --> pdb=" O ASN X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 183 through 192 removed outlier: 4.186A pdb=" N GLU X 187 " --> pdb=" O THR X 184 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG X 191 " --> pdb=" O SER X 188 " (cutoff:3.500A) removed outlier: 3.799A 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: 4.381A 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: 3.571A pdb=" N ASP X 365 " --> pdb=" O PRO X 361 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG X 366 " --> pdb=" O ASP X 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 361 through 366' Processing helix chain 'X' and resid 377 through 390 Processing helix chain 'X' and resid 397 through 409 Processing helix chain 'X' and resid 412 through 417 Processing helix chain 'X' and resid 420 through 428 Processing helix chain 'X' and resid 436 through 445 Processing helix chain 'X' and resid 449 through 457 Processing helix chain 'Y' and resid 50 through 63 Processing helix chain 'Y' and resid 81 through 92 Processing helix chain 'Y' and resid 113 through 124 removed outlier: 4.085A pdb=" N SER Y 124 " --> pdb=" O ALA Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 173 through 180 Processing helix chain 'Y' and resid 206 through 208 No H-bonds generated for 'chain 'Y' and resid 206 through 208' Processing helix chain 'Y' and resid 241 through 249 removed outlier: 3.560A pdb=" N SER Y 249 " --> pdb=" O ASP Y 245 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 267 through 283 Processing helix chain 'Y' and resid 303 through 311 Processing helix chain 'Y' and resid 340 through 342 No H-bonds generated for 'chain 'Y' and resid 340 through 342' Processing helix chain 'Y' and resid 345 through 349 Processing helix chain 'Y' and resid 361 through 374 Processing helix chain 'Y' and resid 381 through 393 Processing helix chain 'Y' and resid 396 through 413 removed outlier: 3.835A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) Processing helix chain 'Y' and resid 420 through 429 Processing helix chain 'Y' and resid 433 through 446 removed outlier: 3.701A pdb=" N ASN Y 443 " --> pdb=" O TYR Y 439 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER Y 445 " --> pdb=" O GLN Y 441 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLN Y 446 " --> pdb=" O GLU Y 442 " (cutoff:3.500A) Processing helix chain 'Q' and resid 958 through 970 Processing helix chain 'Q' and resid 975 through 984 Processing helix chain 'Q' and resid 1000 through 1012 removed outlier: 3.780A pdb=" N GLN Q1006 " --> pdb=" O ASN Q1002 " (cutoff:3.500A) removed outlier: 3.634A 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 1143 Processing helix chain 'Q' and resid 1148 through 1153 Processing helix chain 'Q' and resid 1170 through 1175 Processing helix chain 'Q' and resid 1177 through 1179 No H-bonds generated for 'chain 'Q' and resid 1177 through 1179' 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 1281 through 1283 No H-bonds generated for 'chain 'Q' and resid 1281 through 1283' Processing helix chain 'Q' and resid 1293 through 1297 Processing helix chain 'Q' and resid 1299 through 1314 removed outlier: 4.362A pdb=" N VAL Q1309 " --> pdb=" O ASP Q1305 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS Q1310 " --> pdb=" O GLU Q1306 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU Q1311 " --> pdb=" O LEU Q1307 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1326 through 1337 Processing helix chain 'Q' and resid 1357 through 1363 Processing helix chain 'Q' and resid 1398 through 1407 Processing helix chain 'Q' and resid 1428 through 1431 No H-bonds generated for 'chain 'Q' and resid 1428 through 1431' Processing sheet with id= A, first strand: chain 'R' and resid 14 through 16 removed outlier: 3.535A pdb=" N VAL R 14 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'R' and resid 40 through 44 Processing sheet with id= C, first strand: chain 'R' and resid 67 through 71 Processing sheet with id= D, first strand: chain 'R' and resid 700 through 702 removed outlier: 6.850A pdb=" N VAL R 668 " --> pdb=" O ASN R 701 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU R 185 " --> pdb=" O LEU R 669 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR R 671 " --> pdb=" O LEU R 185 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE R 187 " --> pdb=" O THR R 671 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 367 through 372 removed outlier: 7.284A pdb=" N ALA T 74 " --> pdb=" O LEU T 368 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N THR T 372 " --> pdb=" O LEU T 76 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA T 78 " --> pdb=" O THR T 372 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL T 336 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU T 77 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU T 338 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N GLY T 79 " --> pdb=" O LEU T 338 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER T 340 " --> pdb=" O GLY T 79 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 301 through 305 Processing sheet with id= G, first strand: chain 'T' and resid 175 through 181 removed outlier: 3.667A pdb=" N GLY T 175 " --> pdb=" O SER T 172 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS T 165 " --> pdb=" O GLU T 150 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU T 150 " --> pdb=" O HIS T 165 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE T 167 " --> pdb=" O THR T 148 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU T 146 " --> pdb=" O GLY T 169 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS T 171 " --> pdb=" O VAL T 144 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL T 144 " --> pdb=" O LYS T 171 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP T 198 " --> pdb=" O VAL T 144 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TYR T 201 " --> pdb=" O ARG T 211 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ARG T 211 " --> pdb=" O TYR T 201 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLU T 203 " --> pdb=" O VAL T 209 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL T 209 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'T' and resid 344 through 346 Processing sheet with id= I, first strand: chain 'U' and resid 351 through 356 removed outlier: 7.054A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N THR U 356 " --> pdb=" O LEU U 72 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA U 74 " --> pdb=" O THR U 356 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL U 321 " --> pdb=" O VAL U 71 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL U 73 " --> pdb=" O VAL U 321 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET U 323 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLY U 75 " --> pdb=" O MET U 323 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR U 325 " --> pdb=" O GLY U 75 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'U' and resid 287 through 290 Processing sheet with id= K, first strand: chain 'U' and resid 166 through 171 removed outlier: 4.139A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS U 161 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL U 140 " --> pdb=" O LYS U 161 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP U 188 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER U 191 " --> pdb=" O LYS U 201 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LYS U 201 " --> pdb=" O SER U 191 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ASP U 193 " --> pdb=" O ILE U 199 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE U 199 " --> pdb=" O ASP U 193 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'U' and resid 329 through 331 Processing sheet with id= M, first strand: chain 'V' and resid 368 through 371 removed outlier: 6.477A pdb=" N VAL V 336 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU V 77 " --> pdb=" O VAL V 336 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU V 338 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V' and resid 301 through 305 Processing sheet with id= O, first strand: chain 'V' and resid 175 through 181 removed outlier: 3.700A pdb=" N GLY V 175 " --> pdb=" O SER V 172 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS V 165 " --> pdb=" O GLU V 150 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU V 146 " --> pdb=" O GLY V 169 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS V 171 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL V 144 " --> pdb=" O LYS V 171 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP V 198 " --> pdb=" O VAL V 144 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR V 201 " --> pdb=" O ARG V 211 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ARG V 211 " --> pdb=" O TYR V 201 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLU V 203 " --> pdb=" O VAL V 209 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL V 209 " --> pdb=" O GLU V 203 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'V' and resid 344 through 346 Processing sheet with id= Q, first strand: chain 'W' and resid 351 through 356 removed outlier: 6.897A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR W 356 " --> pdb=" O LEU W 72 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA W 74 " --> pdb=" O THR W 356 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL W 321 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL W 73 " --> pdb=" O VAL W 321 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET W 323 " --> pdb=" O VAL W 73 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLY W 75 " --> pdb=" O MET W 323 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR W 325 " --> pdb=" O GLY W 75 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'W' and resid 286 through 290 Processing sheet with id= S, first strand: chain 'W' and resid 166 through 171 removed outlier: 3.831A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU W 142 " --> pdb=" O THR W 159 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE W 190 " --> pdb=" O GLY W 138 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASP W 188 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY W 203 " --> pdb=" O VAL W 189 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER W 191 " --> pdb=" O LYS W 201 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LYS W 201 " --> pdb=" O SER W 191 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ASP W 193 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE W 199 " --> pdb=" O ASP W 193 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'X' and resid 367 through 371 removed outlier: 7.049A pdb=" N ALA X 74 " --> pdb=" O LEU X 368 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL X 336 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU X 77 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU X 338 " --> pdb=" O LEU X 77 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 301 through 305 removed outlier: 3.536A pdb=" N VAL X 139 " --> pdb=" O LYS X 239 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS X 239 " --> pdb=" O VAL X 139 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'X' and resid 175 through 181 removed outlier: 3.556A pdb=" N GLY X 175 " --> pdb=" O SER X 172 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL X 166 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS X 165 " --> pdb=" O GLU X 150 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU X 146 " --> pdb=" O GLY X 169 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS X 171 " --> pdb=" O VAL X 144 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL X 144 " --> pdb=" O LYS X 171 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY X 142 " --> pdb=" O ILE X 200 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASP X 198 " --> pdb=" O VAL X 144 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR X 201 " --> pdb=" O ARG X 211 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG X 211 " --> pdb=" O TYR X 201 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 344 through 346 Processing sheet with id= X, first strand: chain 'Y' and resid 352 through 355 removed outlier: 3.682A pdb=" N ILE Y 352 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Y' and resid 287 through 290 removed outlier: 3.640A pdb=" N GLU Y 287 " --> pdb=" O LYS Y 128 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Y' and resid 166 through 171 removed outlier: 3.604A pdb=" N LEU Y 171 " --> pdb=" O GLY Y 156 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU Y 142 " --> pdb=" O THR Y 159 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS Y 161 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N VAL Y 140 " --> pdb=" O LYS Y 161 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP Y 188 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER Y 191 " --> pdb=" O LYS Y 201 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS Y 201 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ASP Y 193 " --> pdb=" O ILE Y 199 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE Y 199 " --> pdb=" O ASP Y 193 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Y' and resid 329 through 331 Processing sheet with id= AB, first strand: chain 'Q' and resid 949 through 954 removed outlier: 6.312A pdb=" N VAL Q1419 " --> pdb=" O ILE Q 950 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL Q 952 " --> pdb=" O VAL Q1419 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG Q1421 " --> pdb=" O VAL Q 952 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N CYS Q 954 " --> pdb=" O ARG Q1421 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU Q1423 " --> pdb=" O CYS Q 954 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 1026 through 1028 Processing sheet with id= AD, first strand: chain 'Q' and resid 1082 through 1084 removed outlier: 6.760A pdb=" N THR Q1220 " --> pdb=" O TYR Q1083 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD 1043 hydrogen bonds defined for protein. 3090 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.48 Time building geometry restraints manager: 11.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9541 1.34 - 1.46: 5841 1.46 - 1.59: 13536 1.59 - 1.71: 18 1.71 - 1.83: 166 Bond restraints: 29102 Sorted by residual: bond pdb=" N TYR Y 212 " pdb=" CA TYR Y 212 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.28e-02 6.10e+03 9.33e+00 bond pdb=" N LEU X 224 " pdb=" CA LEU X 224 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.24e+00 bond pdb=" N GLU X 225 " pdb=" CA GLU X 225 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.23e-02 6.61e+03 8.11e+00 bond pdb=" N LEU Q1383 " pdb=" CA LEU Q1383 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.23e-02 6.61e+03 7.52e+00 bond pdb=" N VAL X 230 " pdb=" CA VAL X 230 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.23e-02 6.61e+03 5.93e+00 ... (remaining 29097 not shown) Histogram of bond angle deviations from ideal: 88.05 - 97.66: 4 97.66 - 107.28: 914 107.28 - 116.89: 20033 116.89 - 126.51: 18135 126.51 - 136.13: 287 Bond angle restraints: 39373 Sorted by residual: angle pdb=" N ALA Q1386 " pdb=" CA ALA Q1386 " pdb=" C ALA Q1386 " ideal model delta sigma weight residual 108.32 88.05 20.27 1.64e+00 3.72e-01 1.53e+02 angle pdb=" N ALA Q1385 " pdb=" CA ALA Q1385 " pdb=" C ALA Q1385 " ideal model delta sigma weight residual 108.63 89.86 18.77 1.60e+00 3.91e-01 1.38e+02 angle pdb=" N ALA Q1386 " pdb=" CA ALA Q1386 " pdb=" CB ALA Q1386 " ideal model delta sigma weight residual 110.57 128.70 -18.13 1.69e+00 3.50e-01 1.15e+02 angle pdb=" N TYR T 462 " pdb=" CA TYR T 462 " pdb=" C TYR T 462 " ideal model delta sigma weight residual 111.39 124.25 -12.86 1.38e+00 5.25e-01 8.69e+01 angle pdb=" CA MET R 714 " pdb=" CB MET R 714 " pdb=" CG MET R 714 " ideal model delta sigma weight residual 114.10 125.57 -11.47 2.00e+00 2.50e-01 3.29e+01 ... (remaining 39368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 17190 35.78 - 71.56: 636 71.56 - 107.33: 47 107.33 - 143.11: 3 143.11 - 178.89: 4 Dihedral angle restraints: 17880 sinusoidal: 7318 harmonic: 10562 Sorted by residual: 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 -60.00 118.89 -178.89 1 2.00e+01 2.50e-03 4.80e+01 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 300.00 137.99 162.01 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP T 501 " pdb=" O3A ADP T 501 " pdb=" PA ADP T 501 " pdb=" PB ADP T 501 " ideal model delta sinusoidal sigma weight residual -60.00 93.12 -153.12 1 2.00e+01 2.50e-03 4.54e+01 ... (remaining 17877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 4478 0.117 - 0.234: 138 0.234 - 0.351: 2 0.351 - 0.469: 0 0.469 - 0.586: 2 Chirality restraints: 4620 Sorted by residual: chirality pdb=" CA ALA Q1385 " pdb=" N ALA Q1385 " pdb=" C ALA Q1385 " pdb=" CB ALA Q1385 " both_signs ideal model delta sigma weight residual False 2.48 3.07 -0.59 2.00e-01 2.50e+01 8.58e+00 chirality pdb=" CA TYR T 462 " pdb=" N TYR T 462 " pdb=" C TYR T 462 " pdb=" CB TYR T 462 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" CB VAL Q1152 " pdb=" CA VAL Q1152 " pdb=" CG1 VAL Q1152 " pdb=" CG2 VAL Q1152 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 4617 not shown) Planarity restraints: 5040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE X 222 " 0.025 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C PHE X 222 " -0.087 2.00e-02 2.50e+03 pdb=" O PHE X 222 " 0.033 2.00e-02 2.50e+03 pdb=" N ASP X 223 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA S 148 " -0.069 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO S 149 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO S 149 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO S 149 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP S 69 " -0.015 2.00e-02 2.50e+03 3.13e-02 9.77e+00 pdb=" CG ASP S 69 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP S 69 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP S 69 " -0.019 2.00e-02 2.50e+03 ... (remaining 5037 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 9 2.24 - 2.91: 11150 2.91 - 3.57: 39187 3.57 - 4.24: 64764 4.24 - 4.90: 111970 Nonbonded interactions: 227080 Sorted by model distance: nonbonded pdb=" CE1 TYR W 212 " pdb=" NH2 ARG X 180 " model vdw 1.580 3.420 nonbonded pdb=" CH2 TRP Q1361 " pdb=" O ALA Q1385 " model vdw 1.735 3.340 nonbonded pdb=" O ARG V 413 " pdb=" OE1 GLN V 417 " model vdw 1.834 3.040 nonbonded pdb=" CZ2 TRP Q1361 " pdb=" O ALA Q1385 " model vdw 1.856 3.340 nonbonded pdb=" CD1 ILE W 303 " pdb=" CG2 THR W 335 " model vdw 2.152 3.880 ... (remaining 227075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'T' and (resid 22 through 463 or resid 501)) selection = (chain 'V' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 463 or resid 501)) selection = (chain 'X' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 463 or resid 501)) } ncs_group { reference = (chain 'U' and (resid 18 through 459 or resid 501)) selection = (chain 'W' and (resid 18 through 210 or resid 221 through 459 or resid 501)) selection = (chain 'Y' and (resid 18 through 210 or resid 221 through 459 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 23.140 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 70.670 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.150 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:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 0.062 29102 Z= 0.321 Angle : 0.921 20.273 39373 Z= 0.481 Chirality : 0.052 0.586 4620 Planarity : 0.006 0.105 5040 Dihedral : 17.824 178.892 11060 Min Nonbonded Distance : 1.580 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.06 % Allowed : 26.13 % Favored : 73.81 % 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: -1.69 (0.12), residues: 3618 helix: -1.44 (0.11), residues: 1475 sheet: 0.58 (0.20), residues: 672 loop : -1.46 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Q1361 HIS 0.022 0.001 HIS U 153 PHE 0.035 0.002 PHE S 32 TYR 0.022 0.002 TYR V 462 ARG 0.010 0.001 ARG Q1431 *********************** 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 943 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 941 time to evaluate : 3.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.7596 (p0) cc_final: 0.7272 (p0) REVERT: R 38 SER cc_start: 0.7797 (t) cc_final: 0.7530 (m) REVERT: R 69 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7756 (mtpt) REVERT: R 95 GLN cc_start: 0.8166 (mt0) cc_final: 0.7698 (mt0) REVERT: R 97 ARG cc_start: 0.7509 (ttp-110) cc_final: 0.7060 (ttp-110) REVERT: R 112 GLU cc_start: 0.6960 (tt0) cc_final: 0.6651 (tt0) REVERT: R 121 HIS cc_start: 0.8310 (m-70) cc_final: 0.7971 (m-70) REVERT: R 144 GLN cc_start: 0.7226 (pm20) cc_final: 0.6393 (pm20) REVERT: R 193 ASP cc_start: 0.7376 (p0) cc_final: 0.7047 (p0) REVERT: R 249 ASP cc_start: 0.7708 (m-30) cc_final: 0.7171 (m-30) REVERT: R 262 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7421 (mm-30) REVERT: R 275 VAL cc_start: 0.7843 (t) cc_final: 0.7419 (m) REVERT: R 277 VAL cc_start: 0.7507 (m) cc_final: 0.7059 (p) REVERT: R 601 HIS cc_start: 0.7000 (t70) cc_final: 0.6643 (t70) REVERT: R 608 GLU cc_start: 0.7167 (tt0) cc_final: 0.6640 (tt0) REVERT: R 609 GLN cc_start: 0.7814 (mt0) cc_final: 0.7487 (mt0) REVERT: R 615 ASN cc_start: 0.8366 (p0) cc_final: 0.8114 (p0) REVERT: R 623 GLU cc_start: 0.8082 (tp30) cc_final: 0.7669 (tm-30) REVERT: R 659 GLN cc_start: 0.6976 (mm-40) cc_final: 0.6684 (mm-40) REVERT: R 681 LYS cc_start: 0.8023 (ttpt) cc_final: 0.7802 (ttpp) REVERT: R 697 ASN cc_start: 0.8146 (m-40) cc_final: 0.7879 (m110) REVERT: R 705 ASP cc_start: 0.7315 (t0) cc_final: 0.7071 (t0) REVERT: R 733 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7104 (mp0) REVERT: R 743 LYS cc_start: 0.7466 (tptm) cc_final: 0.7071 (tttp) REVERT: R 744 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7985 (mt-10) REVERT: R 751 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7479 (ttpt) REVERT: T 31 LYS cc_start: 0.8391 (mmtp) cc_final: 0.7966 (mmtt) REVERT: T 37 GLU cc_start: 0.7134 (pm20) cc_final: 0.6854 (pm20) REVERT: T 141 GLU cc_start: 0.7945 (tp30) cc_final: 0.7598 (mm-30) REVERT: T 146 GLU cc_start: 0.7935 (tt0) cc_final: 0.7654 (tt0) REVERT: T 167 ILE cc_start: 0.8145 (mp) cc_final: 0.7822 (mp) REVERT: T 180 ARG cc_start: 0.7778 (mtp-110) cc_final: 0.7416 (mtt-85) REVERT: T 187 GLU cc_start: 0.6708 (tp30) cc_final: 0.6305 (tp30) REVERT: T 205 ASN cc_start: 0.7524 (m-40) cc_final: 0.7168 (m-40) REVERT: T 206 THR cc_start: 0.7644 (m) cc_final: 0.6644 (p) REVERT: T 227 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7292 (mt-10) REVERT: T 234 LYS cc_start: 0.8407 (mmmm) cc_final: 0.7927 (mmmm) REVERT: T 269 MET cc_start: 0.6760 (mmm) cc_final: 0.6380 (mmm) REVERT: T 279 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7624 (mt-10) REVERT: T 282 GLU cc_start: 0.7331 (pm20) cc_final: 0.7054 (pm20) REVERT: T 294 LYS cc_start: 0.7952 (ttmm) cc_final: 0.7693 (ttpt) REVERT: T 312 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7880 (mp0) REVERT: T 345 THR cc_start: 0.8298 (m) cc_final: 0.7845 (p) REVERT: T 386 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7449 (mpt180) REVERT: T 392 ARG cc_start: 0.7594 (mtm110) cc_final: 0.6974 (mtm-85) REVERT: T 393 LEU cc_start: 0.7659 (mt) cc_final: 0.7437 (mt) REVERT: T 429 SER cc_start: 0.8061 (t) cc_final: 0.7846 (m) REVERT: T 432 LYS cc_start: 0.8228 (pmtt) cc_final: 0.7938 (pmtt) REVERT: T 441 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7285 (tt0) REVERT: T 454 LYS cc_start: 0.7703 (tttt) cc_final: 0.7496 (ttmm) REVERT: U 32 ASP cc_start: 0.7544 (m-30) cc_final: 0.7202 (m-30) REVERT: U 36 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7293 (mm110) REVERT: U 65 THR cc_start: 0.7995 (p) cc_final: 0.7763 (t) REVERT: U 90 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7649 (mm-40) REVERT: U 105 GLU cc_start: 0.7776 (tt0) cc_final: 0.7434 (mt-10) REVERT: U 110 GLU cc_start: 0.7604 (pp20) cc_final: 0.7175 (pp20) REVERT: U 142 GLU cc_start: 0.7679 (tt0) cc_final: 0.7061 (tm-30) REVERT: U 164 ASP cc_start: 0.8116 (m-30) cc_final: 0.7896 (m-30) REVERT: U 170 GLU cc_start: 0.7766 (tt0) cc_final: 0.7482 (tp30) REVERT: U 174 LYS cc_start: 0.7599 (mtpt) cc_final: 0.7382 (mtpt) REVERT: U 282 GLU cc_start: 0.7706 (tp30) cc_final: 0.7494 (tp30) REVERT: U 285 LYS cc_start: 0.8176 (mttp) cc_final: 0.7863 (mttm) REVERT: U 296 ASP cc_start: 0.8144 (t0) cc_final: 0.7858 (t70) REVERT: U 297 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7958 (mp0) REVERT: U 323 MET cc_start: 0.8781 (mtm) cc_final: 0.8563 (mtp) REVERT: U 327 ARG cc_start: 0.8064 (mmm160) cc_final: 0.7842 (mmm160) REVERT: U 373 GLN cc_start: 0.7649 (mt0) cc_final: 0.7371 (mt0) REVERT: U 374 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7147 (mm-30) REVERT: U 376 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6891 (mm-30) REVERT: U 393 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6961 (tp30) REVERT: U 395 SER cc_start: 0.8113 (t) cc_final: 0.7402 (p) REVERT: U 407 GLN cc_start: 0.8000 (tt0) cc_final: 0.7698 (tp40) REVERT: U 438 LYS cc_start: 0.7904 (ttpp) cc_final: 0.7628 (ttmm) REVERT: U 451 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7661 (mp-120) REVERT: V 23 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7437 (ttt-90) REVERT: V 36 ASP cc_start: 0.7455 (m-30) cc_final: 0.7148 (m-30) REVERT: V 42 LYS cc_start: 0.7806 (mtmm) cc_final: 0.7231 (tttm) REVERT: V 148 THR cc_start: 0.8154 (m) cc_final: 0.7617 (p) REVERT: V 154 ASN cc_start: 0.7338 (t0) cc_final: 0.6911 (t0) REVERT: V 177 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8114 (tttm) REVERT: V 190 GLN cc_start: 0.7981 (tt0) cc_final: 0.7651 (tt0) REVERT: V 214 ARG cc_start: 0.7667 (mmt180) cc_final: 0.7250 (mmt180) REVERT: V 216 ASP cc_start: 0.7066 (p0) cc_final: 0.6673 (p0) REVERT: V 221 GLU cc_start: 0.7030 (pm20) cc_final: 0.6819 (tm-30) REVERT: V 227 GLU cc_start: 0.7764 (tt0) cc_final: 0.7535 (mt-10) REVERT: V 236 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7859 (mt-10) REVERT: V 287 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7581 (mm-30) REVERT: V 294 LYS cc_start: 0.7694 (ttpp) cc_final: 0.7463 (ttpp) REVERT: V 298 GLN cc_start: 0.7684 (mp10) cc_final: 0.7153 (mp10) REVERT: V 376 ASP cc_start: 0.6983 (m-30) cc_final: 0.6738 (m-30) REVERT: V 385 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7059 (mm-30) REVERT: V 394 GLN cc_start: 0.7919 (pt0) cc_final: 0.7527 (pt0) REVERT: V 427 GLN cc_start: 0.7750 (tp40) cc_final: 0.7498 (tp40) REVERT: V 432 LYS cc_start: 0.7483 (mttt) cc_final: 0.7061 (tppt) REVERT: W 36 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7353 (mm-40) REVERT: W 107 PHE cc_start: 0.8566 (m-80) cc_final: 0.8308 (m-80) REVERT: W 130 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7549 (ttpp) REVERT: W 170 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7737 (mt-10) REVERT: W 181 LYS cc_start: 0.7837 (ttpp) cc_final: 0.7277 (ttmt) REVERT: W 182 GLU cc_start: 0.7488 (tp30) cc_final: 0.6807 (pp20) REVERT: W 188 ASP cc_start: 0.7429 (m-30) cc_final: 0.7159 (m-30) REVERT: W 198 LYS cc_start: 0.8344 (tttt) cc_final: 0.8118 (tttt) REVERT: W 252 GLN cc_start: 0.7932 (mt0) cc_final: 0.7622 (tp40) REVERT: W 261 ASP cc_start: 0.8120 (t0) cc_final: 0.7891 (t70) REVERT: W 285 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7842 (ttpp) REVERT: W 300 MET cc_start: 0.8172 (mmm) cc_final: 0.7959 (mmm) REVERT: W 374 GLU cc_start: 0.7192 (tp30) cc_final: 0.6725 (tp30) REVERT: W 378 GLU cc_start: 0.7625 (mp0) cc_final: 0.7179 (mm-30) REVERT: W 381 SER cc_start: 0.7033 (m) cc_final: 0.6778 (p) REVERT: W 385 ASP cc_start: 0.7369 (m-30) cc_final: 0.6910 (m-30) REVERT: W 422 ASP cc_start: 0.8142 (m-30) cc_final: 0.7895 (m-30) REVERT: W 425 ARG cc_start: 0.7618 (ttt90) cc_final: 0.7295 (ttt180) REVERT: W 433 SER cc_start: 0.7133 (t) cc_final: 0.6837 (m) REVERT: W 438 LYS cc_start: 0.7544 (ttmt) cc_final: 0.7286 (ttmm) REVERT: W 444 GLU cc_start: 0.7275 (mt-10) cc_final: 0.7070 (mt-10) REVERT: W 449 ASP cc_start: 0.7382 (t70) cc_final: 0.7004 (t70) REVERT: W 451 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7492 (mm-40) REVERT: W 455 GLN cc_start: 0.7404 (mm110) cc_final: 0.7057 (tt0) REVERT: X 37 GLU cc_start: 0.7582 (pp20) cc_final: 0.7279 (pp20) REVERT: X 63 ASP cc_start: 0.8001 (m-30) cc_final: 0.7759 (m-30) REVERT: X 125 PHE cc_start: 0.7797 (t80) cc_final: 0.7576 (t80) REVERT: X 134 LYS cc_start: 0.7800 (ptpt) cc_final: 0.7495 (ptpp) REVERT: X 138 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7522 (mm-30) REVERT: X 140 TYR cc_start: 0.7857 (m-80) cc_final: 0.7466 (m-80) REVERT: X 150 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6954 (tt0) REVERT: X 156 LEU cc_start: 0.8650 (mt) cc_final: 0.8356 (mp) REVERT: X 177 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7744 (ttmm) REVERT: X 182 ASP cc_start: 0.8247 (t70) cc_final: 0.7714 (t0) REVERT: X 192 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7529 (mm-30) REVERT: X 196 ILE cc_start: 0.8202 (mt) cc_final: 0.7903 (mp) REVERT: X 218 TYR cc_start: 0.8076 (m-80) cc_final: 0.7560 (m-80) REVERT: X 221 GLU cc_start: 0.7551 (tp30) cc_final: 0.7154 (tt0) REVERT: X 229 TYR cc_start: 0.7400 (m-80) cc_final: 0.6603 (m-80) REVERT: X 232 LEU cc_start: 0.8702 (tt) cc_final: 0.8438 (tm) REVERT: X 242 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7474 (mp0) REVERT: X 243 ILE cc_start: 0.7588 (mt) cc_final: 0.7364 (mm) REVERT: X 282 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6777 (tm-30) REVERT: X 286 GLN cc_start: 0.7611 (mm110) cc_final: 0.7269 (mm110) REVERT: X 295 TYR cc_start: 0.7661 (m-80) cc_final: 0.7454 (m-80) REVERT: X 302 GLU cc_start: 0.7767 (tp30) cc_final: 0.7435 (tp30) REVERT: X 317 ASP cc_start: 0.7183 (t0) cc_final: 0.6894 (m-30) REVERT: X 341 ASN cc_start: 0.8301 (p0) cc_final: 0.7936 (p0) REVERT: X 351 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6968 (mm-30) REVERT: X 390 VAL cc_start: 0.7487 (t) cc_final: 0.7277 (p) REVERT: X 429 SER cc_start: 0.7911 (t) cc_final: 0.7443 (p) REVERT: Y 59 LYS cc_start: 0.7916 (tppt) cc_final: 0.7499 (tppp) REVERT: Y 69 ARG cc_start: 0.7916 (mtt90) cc_final: 0.7470 (mmm-85) REVERT: Y 110 GLU cc_start: 0.7617 (pt0) cc_final: 0.7394 (pt0) REVERT: Y 130 LYS cc_start: 0.8198 (ttmm) cc_final: 0.7980 (ttpp) REVERT: Y 165 MET cc_start: 0.8321 (ptp) cc_final: 0.7749 (ppp) REVERT: Y 202 LEU cc_start: 0.8338 (mm) cc_final: 0.8089 (mp) REVERT: Y 226 GLU cc_start: 0.7367 (mp0) cc_final: 0.7041 (mp0) REVERT: Y 233 LYS cc_start: 0.7385 (ttmt) cc_final: 0.7130 (ttpp) REVERT: Y 236 VAL cc_start: 0.8344 (m) cc_final: 0.8121 (t) REVERT: Y 266 ARG cc_start: 0.7555 (mtm110) cc_final: 0.7291 (mtm110) REVERT: Y 282 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7573 (tm-30) REVERT: Y 287 GLU cc_start: 0.7688 (pt0) cc_final: 0.7117 (pm20) REVERT: Y 297 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8082 (mm-30) REVERT: Y 317 PHE cc_start: 0.8413 (m-80) cc_final: 0.8064 (m-80) REVERT: Y 327 ARG cc_start: 0.8329 (mmt-90) cc_final: 0.8073 (mmt-90) REVERT: Y 331 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7778 (ttpt) REVERT: Y 350 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7222 (mtm-85) REVERT: Y 357 LYS cc_start: 0.8230 (mttm) cc_final: 0.7766 (mmmm) REVERT: Y 374 GLU cc_start: 0.6621 (tt0) cc_final: 0.6245 (tt0) REVERT: Y 376 GLU cc_start: 0.7686 (mp0) cc_final: 0.7426 (mm-30) REVERT: Y 378 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7092 (pm20) REVERT: Y 381 SER cc_start: 0.7115 (m) cc_final: 0.6820 (t) REVERT: Y 417 THR cc_start: 0.7822 (p) cc_final: 0.7396 (t) REVERT: Y 422 ASP cc_start: 0.8098 (m-30) cc_final: 0.7749 (m-30) REVERT: Y 439 TYR cc_start: 0.7861 (m-80) cc_final: 0.7233 (m-80) REVERT: Y 444 GLU cc_start: 0.7925 (tt0) cc_final: 0.7347 (tp30) REVERT: Q 1072 ASP cc_start: 0.8038 (m-30) cc_final: 0.7779 (m-30) REVERT: Q 1078 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7381 (mtm-85) REVERT: Q 1083 TYR cc_start: 0.8208 (t80) cc_final: 0.7963 (t80) REVERT: Q 1103 ASP cc_start: 0.7689 (p0) cc_final: 0.6362 (p0) REVERT: Q 1106 ASN cc_start: 0.7906 (t0) cc_final: 0.7667 (t0) REVERT: Q 1123 GLU cc_start: 0.7691 (mp0) cc_final: 0.7449 (mp0) REVERT: Q 1134 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7408 (mm-30) REVERT: Q 1146 THR cc_start: 0.7240 (p) cc_final: 0.5854 (m) REVERT: Q 1226 SER cc_start: 0.8269 (t) cc_final: 0.8048 (t) REVERT: Q 1231 ASN cc_start: 0.7794 (m-40) cc_final: 0.7438 (m-40) REVERT: Q 1239 ASP cc_start: 0.7131 (t0) cc_final: 0.6808 (t70) REVERT: Q 1260 LYS cc_start: 0.8475 (mtpp) cc_final: 0.8089 (mtpp) REVERT: Q 1266 GLU cc_start: 0.7651 (mp0) cc_final: 0.7042 (mp0) REVERT: Q 1280 LYS cc_start: 0.8046 (ptpp) cc_final: 0.7729 (ptpp) REVERT: Q 1301 LEU cc_start: 0.7155 (tp) cc_final: 0.6910 (tt) REVERT: Q 1305 ASP cc_start: 0.7705 (m-30) cc_final: 0.7295 (m-30) outliers start: 2 outliers final: 1 residues processed: 941 average time/residue: 1.6212 time to fit residues: 1742.6521 Evaluate side-chains 818 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 817 time to evaluate : 3.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 196 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 0.7980 chunk 273 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 210 optimal weight: 0.5980 chunk 327 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 121 HIS R 146 GLN R 633 GLN S 162 ASN U 144 GLN U 237 HIS U 272 GLN U 441 GLN U 446 GLN U 455 GLN V 51 GLN V 263 GLN V 331 ASN V 417 GLN W 144 GLN W 155 GLN W 173 ASN X 51 GLN X 271 GLN X 314 ASN X 325 ASN Y 248 ASN Y 310 ASN Q1211 HIS Q1244 GLN Q1316 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29102 Z= 0.258 Angle : 0.603 8.254 39373 Z= 0.300 Chirality : 0.044 0.173 4620 Planarity : 0.004 0.073 5040 Dihedral : 7.714 142.386 4006 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.29 % Allowed : 26.16 % Favored : 70.55 % 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: -0.66 (0.13), residues: 3618 helix: -0.12 (0.13), residues: 1485 sheet: 0.60 (0.20), residues: 670 loop : -1.17 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q1361 HIS 0.005 0.001 HIS Q1211 PHE 0.024 0.001 PHE R 691 TYR 0.022 0.002 TYR R 724 ARG 0.009 0.000 ARG V 371 *********************** 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 947 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 843 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.7856 (p0) cc_final: 0.7155 (p0) REVERT: R 38 SER cc_start: 0.7989 (t) cc_final: 0.7532 (m) REVERT: R 69 LYS cc_start: 0.7948 (mtpt) cc_final: 0.7689 (mtpt) REVERT: R 70 PHE cc_start: 0.7115 (t80) cc_final: 0.6804 (t80) REVERT: R 74 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8377 (pptt) REVERT: R 93 ARG cc_start: 0.8419 (ttm170) cc_final: 0.8176 (ttm-80) REVERT: R 95 GLN cc_start: 0.8244 (mt0) cc_final: 0.7758 (mt0) REVERT: R 101 ASP cc_start: 0.7568 (t70) cc_final: 0.6804 (p0) REVERT: R 112 GLU cc_start: 0.6903 (tt0) cc_final: 0.6678 (tt0) REVERT: R 121 HIS cc_start: 0.8307 (m90) cc_final: 0.8008 (m-70) REVERT: R 144 GLN cc_start: 0.6637 (pm20) cc_final: 0.6414 (pm20) REVERT: R 193 ASP cc_start: 0.7201 (p0) cc_final: 0.6959 (p0) REVERT: R 249 ASP cc_start: 0.7671 (m-30) cc_final: 0.7150 (m-30) REVERT: R 277 VAL cc_start: 0.7691 (m) cc_final: 0.7250 (p) REVERT: R 609 GLN cc_start: 0.7821 (mt0) cc_final: 0.7481 (mt0) REVERT: R 643 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7535 (tm-30) REVERT: R 648 LYS cc_start: 0.8278 (mtpp) cc_final: 0.8063 (mtpp) REVERT: R 659 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6789 (mm-40) REVERT: R 681 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7869 (ttpp) REVERT: R 697 ASN cc_start: 0.8162 (m-40) cc_final: 0.7907 (m110) REVERT: R 705 ASP cc_start: 0.7300 (t0) cc_final: 0.7067 (t0) REVERT: R 733 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7007 (mp0) REVERT: R 743 LYS cc_start: 0.7575 (tptm) cc_final: 0.7076 (tttp) REVERT: R 744 GLU cc_start: 0.8243 (mt-10) cc_final: 0.8025 (mt-10) REVERT: R 751 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7541 (ttpt) REVERT: S 77 LEU cc_start: 0.8199 (mp) cc_final: 0.7957 (mt) REVERT: S 80 LYS cc_start: 0.8390 (tmmt) cc_final: 0.8126 (tmmt) REVERT: T 31 LYS cc_start: 0.8409 (mmtp) cc_final: 0.8004 (mmtt) REVERT: T 37 GLU cc_start: 0.7120 (pm20) cc_final: 0.6821 (pm20) REVERT: T 76 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7941 (tp) REVERT: T 119 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6796 (tm-30) REVERT: T 141 GLU cc_start: 0.7890 (tp30) cc_final: 0.7546 (tp30) REVERT: T 146 GLU cc_start: 0.7732 (tt0) cc_final: 0.7487 (tt0) REVERT: T 187 GLU cc_start: 0.6551 (tp30) cc_final: 0.6054 (tp30) REVERT: T 205 ASN cc_start: 0.7547 (m-40) cc_final: 0.6953 (m-40) REVERT: T 206 THR cc_start: 0.7630 (m) cc_final: 0.6883 (p) REVERT: T 234 LYS cc_start: 0.8356 (mmmm) cc_final: 0.7834 (mmmm) REVERT: T 236 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8350 (mt-10) REVERT: T 279 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7559 (mt-10) REVERT: T 282 GLU cc_start: 0.7269 (pm20) cc_final: 0.7046 (pm20) REVERT: T 294 LYS cc_start: 0.7882 (ttmm) cc_final: 0.7670 (ttpt) REVERT: T 312 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7965 (mp0) REVERT: T 386 ARG cc_start: 0.7770 (ttm-80) cc_final: 0.7419 (mpt180) REVERT: T 392 ARG cc_start: 0.7594 (mtm110) cc_final: 0.6982 (mtm-85) REVERT: T 393 LEU cc_start: 0.7664 (mt) cc_final: 0.7452 (mt) REVERT: T 432 LYS cc_start: 0.8237 (pmtt) cc_final: 0.7987 (pmtt) REVERT: T 441 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7336 (tt0) REVERT: T 454 LYS cc_start: 0.7721 (tttt) cc_final: 0.7465 (mtpp) REVERT: U 32 ASP cc_start: 0.7596 (m-30) cc_final: 0.7302 (m-30) REVERT: U 36 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7405 (mm110) REVERT: U 71 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7903 (p) REVERT: U 90 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7597 (mm-40) REVERT: U 105 GLU cc_start: 0.7830 (tt0) cc_final: 0.7529 (mt-10) REVERT: U 110 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7083 (pp20) REVERT: U 125 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8102 (mt) REVERT: U 142 GLU cc_start: 0.7630 (tt0) cc_final: 0.6989 (tm-30) REVERT: U 144 GLN cc_start: 0.7968 (mt0) cc_final: 0.7496 (mt0) REVERT: U 164 ASP cc_start: 0.8149 (m-30) cc_final: 0.7907 (m-30) REVERT: U 170 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7436 (tp30) REVERT: U 174 LYS cc_start: 0.7537 (mtpt) cc_final: 0.7302 (mtpt) REVERT: U 200 THR cc_start: 0.8173 (p) cc_final: 0.7919 (t) REVERT: U 237 HIS cc_start: 0.8002 (m-70) cc_final: 0.7776 (m90) REVERT: U 282 GLU cc_start: 0.7732 (tp30) cc_final: 0.7519 (tp30) REVERT: U 296 ASP cc_start: 0.8147 (t0) cc_final: 0.7893 (t70) REVERT: U 297 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8069 (mp0) REVERT: U 323 MET cc_start: 0.8762 (mtm) cc_final: 0.8537 (mtp) REVERT: U 373 GLN cc_start: 0.7577 (mt0) cc_final: 0.7281 (mt0) REVERT: U 376 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6815 (mm-30) REVERT: U 393 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6972 (tp30) REVERT: U 407 GLN cc_start: 0.7965 (tt0) cc_final: 0.7690 (tp40) REVERT: U 438 LYS cc_start: 0.7923 (ttpp) cc_final: 0.7617 (ttmm) REVERT: U 451 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7621 (mp-120) REVERT: V 23 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7374 (ttt-90) REVERT: V 36 ASP cc_start: 0.7615 (m-30) cc_final: 0.7020 (m-30) REVERT: V 42 LYS cc_start: 0.7741 (mtmm) cc_final: 0.7188 (tttm) REVERT: V 122 MET cc_start: 0.8066 (tpp) cc_final: 0.7792 (tpp) REVERT: V 135 GLU cc_start: 0.7784 (tt0) cc_final: 0.7368 (tt0) REVERT: V 148 THR cc_start: 0.8082 (m) cc_final: 0.7476 (p) REVERT: V 154 ASN cc_start: 0.7400 (t0) cc_final: 0.7016 (t0) REVERT: V 161 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7973 (ttmm) REVERT: V 177 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8177 (tttm) REVERT: V 190 GLN cc_start: 0.7927 (tt0) cc_final: 0.7629 (tt0) REVERT: V 203 GLU cc_start: 0.8039 (tt0) cc_final: 0.7644 (tt0) REVERT: V 214 ARG cc_start: 0.7484 (mmt180) cc_final: 0.7104 (mmp-170) REVERT: V 236 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7578 (mm-30) REVERT: V 268 MET cc_start: 0.7690 (mmm) cc_final: 0.7136 (mmm) REVERT: V 269 MET cc_start: 0.8123 (mmp) cc_final: 0.7849 (mmm) REVERT: V 287 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7578 (mm-30) REVERT: V 354 ILE cc_start: 0.7821 (mt) cc_final: 0.7597 (mm) REVERT: V 385 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7241 (mm-30) REVERT: V 394 GLN cc_start: 0.7798 (pt0) cc_final: 0.7459 (pt0) REVERT: V 432 LYS cc_start: 0.7679 (mttt) cc_final: 0.7294 (mtpp) REVERT: W 36 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7388 (mm-40) REVERT: W 107 PHE cc_start: 0.8528 (m-80) cc_final: 0.8240 (m-80) REVERT: W 130 LYS cc_start: 0.8036 (ttmm) cc_final: 0.7667 (ttpp) REVERT: W 170 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7716 (mt-10) REVERT: W 181 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7504 (ttpt) REVERT: W 182 GLU cc_start: 0.7540 (tp30) cc_final: 0.6806 (tm-30) REVERT: W 188 ASP cc_start: 0.7392 (m-30) cc_final: 0.6926 (m-30) REVERT: W 198 LYS cc_start: 0.8334 (tttt) cc_final: 0.8112 (tttt) REVERT: W 261 ASP cc_start: 0.8134 (t0) cc_final: 0.7889 (t70) REVERT: W 283 GLU cc_start: 0.6961 (tm-30) cc_final: 0.6606 (tm-30) REVERT: W 285 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7770 (ttpp) REVERT: W 338 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8192 (mttm) REVERT: W 360 ASN cc_start: 0.6992 (t0) cc_final: 0.6642 (t0) REVERT: W 374 GLU cc_start: 0.7180 (tp30) cc_final: 0.6740 (tp30) REVERT: W 378 GLU cc_start: 0.7606 (mp0) cc_final: 0.7348 (mm-30) REVERT: W 381 SER cc_start: 0.7171 (m) cc_final: 0.6892 (p) REVERT: W 385 ASP cc_start: 0.7257 (m-30) cc_final: 0.6858 (m-30) REVERT: W 389 LYS cc_start: 0.7641 (mmmm) cc_final: 0.7362 (mmmm) REVERT: W 393 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6466 (mt-10) REVERT: W 421 GLU cc_start: 0.7578 (mp0) cc_final: 0.7297 (mp0) REVERT: W 425 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7238 (ttt90) REVERT: W 455 GLN cc_start: 0.7392 (mm110) cc_final: 0.7044 (tt0) REVERT: X 37 GLU cc_start: 0.7642 (pp20) cc_final: 0.7309 (pp20) REVERT: X 63 ASP cc_start: 0.7860 (m-30) cc_final: 0.7641 (m-30) REVERT: X 94 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6627 (mt0) REVERT: X 125 PHE cc_start: 0.7848 (t80) cc_final: 0.7535 (t80) REVERT: X 134 LYS cc_start: 0.8084 (ptpt) cc_final: 0.7719 (ptpp) REVERT: X 135 GLU cc_start: 0.7213 (tt0) cc_final: 0.6585 (mt-10) REVERT: X 150 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7120 (tt0) REVERT: X 156 LEU cc_start: 0.8683 (mt) cc_final: 0.8412 (mp) REVERT: X 177 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7869 (ttmm) REVERT: X 180 ARG cc_start: 0.7869 (mtp180) cc_final: 0.7611 (mtp180) REVERT: X 182 ASP cc_start: 0.8173 (t70) cc_final: 0.7629 (t0) REVERT: X 192 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7551 (mm-30) REVERT: X 196 ILE cc_start: 0.8157 (mt) cc_final: 0.7871 (mp) REVERT: X 203 GLU cc_start: 0.5694 (tm-30) cc_final: 0.5174 (tm-30) REVERT: X 206 THR cc_start: 0.7685 (p) cc_final: 0.7233 (t) REVERT: X 221 GLU cc_start: 0.7628 (tp30) cc_final: 0.7207 (tt0) REVERT: X 242 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7489 (mp0) REVERT: X 243 ILE cc_start: 0.7812 (mt) cc_final: 0.7532 (mm) REVERT: X 282 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6873 (tm-30) REVERT: X 302 GLU cc_start: 0.7828 (tp30) cc_final: 0.7504 (tp30) REVERT: X 317 ASP cc_start: 0.7219 (t0) cc_final: 0.6874 (m-30) REVERT: X 341 ASN cc_start: 0.8512 (p0) cc_final: 0.8129 (p0) REVERT: X 351 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6986 (mm-30) REVERT: X 429 SER cc_start: 0.7875 (t) cc_final: 0.7450 (p) REVERT: Y 26 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8118 (mp) REVERT: Y 69 ARG cc_start: 0.8022 (mtt90) cc_final: 0.7649 (mmm-85) REVERT: Y 110 GLU cc_start: 0.7583 (pt0) cc_final: 0.7339 (pt0) REVERT: Y 130 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7966 (ttpp) REVERT: Y 202 LEU cc_start: 0.8234 (mm) cc_final: 0.7880 (mt) REVERT: Y 226 GLU cc_start: 0.7365 (mp0) cc_final: 0.7023 (mp0) REVERT: Y 236 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8168 (t) REVERT: Y 266 ARG cc_start: 0.7452 (mtm110) cc_final: 0.7249 (mtm110) REVERT: Y 282 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7525 (tm-30) REVERT: Y 297 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7746 (mm-30) REVERT: Y 317 PHE cc_start: 0.8478 (m-80) cc_final: 0.8097 (m-80) REVERT: Y 327 ARG cc_start: 0.8317 (mmt-90) cc_final: 0.8048 (mmt-90) REVERT: Y 331 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7779 (ttpp) REVERT: Y 350 ARG cc_start: 0.7694 (mtm-85) cc_final: 0.7106 (mtp85) REVERT: Y 357 LYS cc_start: 0.8343 (mttm) cc_final: 0.7826 (mmmm) REVERT: Y 378 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7026 (pm20) REVERT: Y 392 VAL cc_start: 0.7879 (t) cc_final: 0.7646 (p) REVERT: Y 417 THR cc_start: 0.7877 (p) cc_final: 0.7423 (t) REVERT: Y 419 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7162 (mm-30) REVERT: Y 444 GLU cc_start: 0.7756 (tt0) cc_final: 0.7082 (tm-30) REVERT: Q 1021 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: Q 1030 THR cc_start: 0.8062 (p) cc_final: 0.6983 (p) REVERT: Q 1078 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7341 (mtm-85) REVERT: Q 1103 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.6927 (p0) REVERT: Q 1123 GLU cc_start: 0.7665 (mp0) cc_final: 0.7379 (mp0) REVERT: Q 1134 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7489 (mm-30) REVERT: Q 1146 THR cc_start: 0.7264 (p) cc_final: 0.7023 (p) REVERT: Q 1160 LYS cc_start: 0.7618 (ptpp) cc_final: 0.7354 (ptpp) REVERT: Q 1189 SER cc_start: 0.8006 (t) cc_final: 0.7583 (p) REVERT: Q 1231 ASN cc_start: 0.7802 (m-40) cc_final: 0.7478 (m-40) REVERT: Q 1239 ASP cc_start: 0.7047 (t0) cc_final: 0.6790 (t70) REVERT: Q 1260 LYS cc_start: 0.8425 (mtpp) cc_final: 0.8078 (mtpp) REVERT: Q 1266 GLU cc_start: 0.7635 (mp0) cc_final: 0.7084 (mp0) REVERT: Q 1280 LYS cc_start: 0.8044 (ptpp) cc_final: 0.7738 (ptpp) REVERT: Q 1305 ASP cc_start: 0.7757 (m-30) cc_final: 0.7404 (m-30) REVERT: Q 1405 MET cc_start: 0.6697 (tmm) cc_final: 0.6443 (mmm) REVERT: Z 303 GLU cc_start: 0.7193 (mp0) cc_final: 0.6919 (mp0) REVERT: Z 314 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7709 (pp20) outliers start: 104 outliers final: 36 residues processed: 893 average time/residue: 1.6323 time to fit residues: 1662.2023 Evaluate side-chains 874 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 822 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 132 ASN Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 664 MET Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 236 GLU Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 398 SER Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 161 LYS Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 430 ASN Chi-restraints excluded: chain W residue 233 LYS Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 336 ASN Chi-restraints excluded: chain W residue 338 LYS Chi-restraints excluded: chain W residue 373 GLN Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 454 LYS Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 188 ASP Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1103 ASP Chi-restraints excluded: chain Q residue 1150 LYS Chi-restraints excluded: chain Z residue 314 GLU Chi-restraints excluded: chain Z residue 315 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 328 optimal weight: 1.9990 chunk 354 optimal weight: 0.9990 chunk 292 optimal weight: 3.9990 chunk 325 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 263 optimal weight: 0.3980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 610 HIS R 633 GLN R 749 ASN T 29 HIS ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 331 ASN U 272 GLN U 362 GLN U 441 GLN U 446 GLN U 455 GLN V 263 GLN V 417 GLN ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 173 ASN X 271 GLN X 289 ASN X 325 ASN Y 49 GLN Y 310 ASN Y 373 GLN Q1244 GLN Q1403 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29102 Z= 0.349 Angle : 0.630 9.668 39373 Z= 0.311 Chirality : 0.046 0.160 4620 Planarity : 0.004 0.058 5040 Dihedral : 7.331 134.261 4004 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.06 % Allowed : 25.78 % Favored : 69.16 % 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: -0.37 (0.13), residues: 3618 helix: 0.33 (0.13), residues: 1507 sheet: 0.51 (0.20), residues: 640 loop : -1.11 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP Y 280 HIS 0.010 0.001 HIS T 165 PHE 0.023 0.002 PHE R 691 TYR 0.024 0.002 TYR V 462 ARG 0.007 0.000 ARG Y 232 *********************** 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: 160 poor density : 854 time to evaluate : 3.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.7870 (p0) cc_final: 0.7208 (p0) REVERT: R 38 SER cc_start: 0.8024 (t) cc_final: 0.7609 (m) REVERT: R 69 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7682 (mtpt) REVERT: R 70 PHE cc_start: 0.7035 (t80) cc_final: 0.6828 (t80) REVERT: R 74 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8375 (pptt) REVERT: R 95 GLN cc_start: 0.8345 (mt0) cc_final: 0.7784 (mt0) REVERT: R 121 HIS cc_start: 0.8408 (m90) cc_final: 0.8015 (m-70) REVERT: R 146 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7213 (mm-40) REVERT: R 193 ASP cc_start: 0.7294 (p0) cc_final: 0.7030 (p0) REVERT: R 249 ASP cc_start: 0.7669 (m-30) cc_final: 0.7147 (m-30) REVERT: R 266 THR cc_start: 0.6650 (m) cc_final: 0.6331 (m) REVERT: R 268 GLU cc_start: 0.7658 (pm20) cc_final: 0.7360 (pm20) REVERT: R 609 GLN cc_start: 0.7826 (mt0) cc_final: 0.7530 (mt0) REVERT: R 617 GLU cc_start: 0.8160 (mp0) cc_final: 0.7766 (mp0) REVERT: R 623 GLU cc_start: 0.8176 (tp30) cc_final: 0.7357 (tm-30) REVERT: R 643 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7553 (tm-30) REVERT: R 659 GLN cc_start: 0.7260 (mm-40) cc_final: 0.6962 (mm-40) REVERT: R 697 ASN cc_start: 0.8185 (m-40) cc_final: 0.7897 (m110) REVERT: R 705 ASP cc_start: 0.7300 (t0) cc_final: 0.7042 (t0) REVERT: R 733 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6970 (mp0) REVERT: R 743 LYS cc_start: 0.7623 (tptm) cc_final: 0.7062 (tttp) REVERT: R 744 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8047 (mt-10) REVERT: R 751 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7560 (ttpt) REVERT: S 77 LEU cc_start: 0.8181 (mp) cc_final: 0.7900 (mt) REVERT: S 80 LYS cc_start: 0.8409 (tmmt) cc_final: 0.8178 (tmmt) REVERT: S 141 GLN cc_start: 0.7287 (mm-40) cc_final: 0.6967 (mm-40) REVERT: T 31 LYS cc_start: 0.8407 (mmtp) cc_final: 0.8018 (mmtt) REVERT: T 76 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7912 (tp) REVERT: T 141 GLU cc_start: 0.7931 (tp30) cc_final: 0.7511 (tp30) REVERT: T 146 GLU cc_start: 0.7796 (tt0) cc_final: 0.7554 (tt0) REVERT: T 205 ASN cc_start: 0.7438 (m-40) cc_final: 0.7036 (m-40) REVERT: T 206 THR cc_start: 0.7769 (m) cc_final: 0.7278 (p) REVERT: T 234 LYS cc_start: 0.8322 (mmmm) cc_final: 0.7790 (mmmm) REVERT: T 236 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8360 (mt-10) REVERT: T 279 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7461 (mt-10) REVERT: T 282 GLU cc_start: 0.7241 (pm20) cc_final: 0.6952 (pm20) REVERT: T 294 LYS cc_start: 0.7870 (ttmm) cc_final: 0.7666 (ttpt) REVERT: T 312 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7910 (mp0) REVERT: T 386 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7394 (mpt180) REVERT: T 392 ARG cc_start: 0.7565 (mtm110) cc_final: 0.7106 (mtm-85) REVERT: T 393 LEU cc_start: 0.7705 (mt) cc_final: 0.7495 (mt) REVERT: T 413 ARG cc_start: 0.7184 (mtt180) cc_final: 0.6901 (mtt180) REVERT: T 432 LYS cc_start: 0.8235 (pmtt) cc_final: 0.7989 (pmtt) REVERT: T 441 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7239 (tt0) REVERT: U 32 ASP cc_start: 0.7637 (m-30) cc_final: 0.7347 (m-30) REVERT: U 36 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7478 (mm110) REVERT: U 71 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7883 (p) REVERT: U 90 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7507 (mm-40) REVERT: U 105 GLU cc_start: 0.7911 (tt0) cc_final: 0.7561 (mt-10) REVERT: U 110 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6929 (pp20) REVERT: U 125 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8124 (mt) REVERT: U 127 ILE cc_start: 0.8537 (mt) cc_final: 0.8334 (mp) REVERT: U 142 GLU cc_start: 0.7599 (tt0) cc_final: 0.7093 (tm-30) REVERT: U 144 GLN cc_start: 0.7867 (mt0) cc_final: 0.7627 (mt0) REVERT: U 164 ASP cc_start: 0.8108 (m-30) cc_final: 0.7663 (m-30) REVERT: U 170 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7361 (tp30) REVERT: U 174 LYS cc_start: 0.7517 (mtpt) cc_final: 0.7299 (mtpt) REVERT: U 193 ASP cc_start: 0.8133 (t0) cc_final: 0.7532 (t0) REVERT: U 237 HIS cc_start: 0.8223 (m-70) cc_final: 0.7969 (m-70) REVERT: U 255 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7579 (mp) REVERT: U 282 GLU cc_start: 0.7755 (tp30) cc_final: 0.7452 (tp30) REVERT: U 297 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8129 (mp0) REVERT: U 393 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6982 (tp30) REVERT: U 451 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7618 (mp-120) REVERT: V 23 ARG cc_start: 0.7868 (ttp80) cc_final: 0.7386 (ttt-90) REVERT: V 36 ASP cc_start: 0.7585 (m-30) cc_final: 0.7166 (p0) REVERT: V 42 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7067 (tttm) REVERT: V 111 TYR cc_start: 0.8308 (m-80) cc_final: 0.8033 (m-80) REVERT: V 135 GLU cc_start: 0.7791 (tt0) cc_final: 0.7358 (tt0) REVERT: V 144 VAL cc_start: 0.8167 (t) cc_final: 0.7859 (m) REVERT: V 148 THR cc_start: 0.8078 (m) cc_final: 0.7489 (p) REVERT: V 154 ASN cc_start: 0.7536 (t0) cc_final: 0.7178 (t0) REVERT: V 161 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8159 (ttmm) REVERT: V 203 GLU cc_start: 0.8076 (tt0) cc_final: 0.7633 (tt0) REVERT: V 214 ARG cc_start: 0.7559 (mmt180) cc_final: 0.7083 (mmp-170) REVERT: V 216 ASP cc_start: 0.7121 (p0) cc_final: 0.6821 (p0) REVERT: V 221 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6875 (tm-30) REVERT: V 236 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7627 (mm-30) REVERT: V 268 MET cc_start: 0.7641 (mmm) cc_final: 0.7241 (mmm) REVERT: V 287 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7585 (mm-30) REVERT: V 290 LYS cc_start: 0.7645 (mtpp) cc_final: 0.7431 (mtpm) REVERT: V 311 ASP cc_start: 0.7904 (t0) cc_final: 0.7601 (t0) REVERT: V 317 ASP cc_start: 0.7928 (m-30) cc_final: 0.7390 (m-30) REVERT: V 354 ILE cc_start: 0.7822 (mt) cc_final: 0.7575 (mm) REVERT: W 36 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7378 (mm-40) REVERT: W 130 LYS cc_start: 0.7991 (ttmm) cc_final: 0.7695 (ttpp) REVERT: W 139 GLU cc_start: 0.7947 (tt0) cc_final: 0.7727 (tt0) REVERT: W 181 LYS cc_start: 0.7696 (ttpp) cc_final: 0.7486 (ttmt) REVERT: W 182 GLU cc_start: 0.7532 (tp30) cc_final: 0.7143 (tp30) REVERT: W 198 LYS cc_start: 0.8337 (tttt) cc_final: 0.8098 (tttt) REVERT: W 204 ARG cc_start: 0.7368 (ttt90) cc_final: 0.6862 (ttt90) REVERT: W 220 ARG cc_start: 0.7087 (mpp80) cc_final: 0.6885 (mpp80) REVERT: W 268 GLU cc_start: 0.7612 (mp0) cc_final: 0.7132 (mp0) REVERT: W 283 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6261 (tm-30) REVERT: W 285 LYS cc_start: 0.8083 (ttmm) cc_final: 0.7586 (ttpp) REVERT: W 338 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8208 (mttm) REVERT: W 360 ASN cc_start: 0.7159 (t0) cc_final: 0.6783 (t0) REVERT: W 381 SER cc_start: 0.7368 (m) cc_final: 0.7099 (p) REVERT: W 385 ASP cc_start: 0.7224 (m-30) cc_final: 0.6844 (m-30) REVERT: W 389 LYS cc_start: 0.7640 (mmmm) cc_final: 0.7270 (mmmm) REVERT: W 393 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6460 (mt-10) REVERT: W 425 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7343 (ttt90) REVERT: W 455 GLN cc_start: 0.7357 (mm110) cc_final: 0.7064 (tt0) REVERT: X 37 GLU cc_start: 0.7687 (pp20) cc_final: 0.7330 (pp20) REVERT: X 94 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6749 (mt0) REVERT: X 111 TYR cc_start: 0.8510 (m-80) cc_final: 0.8218 (m-80) REVERT: X 125 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7482 (t80) REVERT: X 134 LYS cc_start: 0.8078 (ptpt) cc_final: 0.7682 (ptpp) REVERT: X 135 GLU cc_start: 0.7231 (tt0) cc_final: 0.6661 (mt-10) REVERT: X 140 TYR cc_start: 0.8161 (m-80) cc_final: 0.7885 (m-80) REVERT: X 143 GLU cc_start: 0.7711 (tt0) cc_final: 0.7327 (tt0) REVERT: X 150 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7150 (tt0) REVERT: X 156 LEU cc_start: 0.8738 (mt) cc_final: 0.8505 (mp) REVERT: X 177 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7857 (ttmm) REVERT: X 180 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7612 (mtp180) REVERT: X 182 ASP cc_start: 0.8190 (t70) cc_final: 0.7573 (t0) REVERT: X 192 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7520 (mm-30) REVERT: X 196 ILE cc_start: 0.8181 (mt) cc_final: 0.7913 (mp) REVERT: X 221 GLU cc_start: 0.7727 (tp30) cc_final: 0.7279 (tt0) REVERT: X 229 TYR cc_start: 0.7666 (m-80) cc_final: 0.7103 (m-80) REVERT: X 242 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7447 (mp0) REVERT: X 243 ILE cc_start: 0.7781 (mt) cc_final: 0.7480 (mp) REVERT: X 282 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6884 (tm-30) REVERT: X 317 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6946 (m-30) REVERT: X 341 ASN cc_start: 0.8560 (p0) cc_final: 0.8134 (p0) REVERT: X 351 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7023 (mm-30) REVERT: X 429 SER cc_start: 0.7815 (t) cc_final: 0.7391 (p) REVERT: Y 26 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8187 (mp) REVERT: Y 69 ARG cc_start: 0.8108 (mtt90) cc_final: 0.7755 (mmm-85) REVERT: Y 106 ILE cc_start: 0.8234 (pp) cc_final: 0.7906 (mp) REVERT: Y 110 GLU cc_start: 0.7511 (pt0) cc_final: 0.7277 (pt0) REVERT: Y 129 ILE cc_start: 0.8231 (mm) cc_final: 0.8009 (mm) REVERT: Y 130 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7943 (ttpp) REVERT: Y 236 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8158 (t) REVERT: Y 282 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7522 (tm-30) REVERT: Y 297 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7734 (mm-30) REVERT: Y 327 ARG cc_start: 0.8394 (mmt-90) cc_final: 0.8194 (mmt-90) REVERT: Y 331 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7838 (ttpt) REVERT: Y 350 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.7238 (mtp85) REVERT: Y 357 LYS cc_start: 0.8428 (mttm) cc_final: 0.8136 (mmmm) REVERT: Y 378 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7145 (mt-10) REVERT: Y 404 SER cc_start: 0.7936 (t) cc_final: 0.7352 (m) REVERT: Y 455 GLN cc_start: 0.8313 (mt0) cc_final: 0.8101 (mt0) REVERT: Q 1021 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7688 (m-30) REVERT: Q 1078 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7468 (mtm-85) REVERT: Q 1092 ASP cc_start: 0.7579 (m-30) cc_final: 0.7279 (m-30) REVERT: Q 1123 GLU cc_start: 0.7656 (mp0) cc_final: 0.7317 (mp0) REVERT: Q 1134 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7527 (mm-30) REVERT: Q 1160 LYS cc_start: 0.7731 (ptpp) cc_final: 0.7394 (ptpp) REVERT: Q 1189 SER cc_start: 0.7964 (t) cc_final: 0.7562 (p) REVERT: Q 1200 ARG cc_start: 0.7695 (mtm110) cc_final: 0.7298 (mtp85) REVERT: Q 1231 ASN cc_start: 0.7837 (m-40) cc_final: 0.7555 (m-40) REVERT: Q 1239 ASP cc_start: 0.7122 (t0) cc_final: 0.6833 (t70) REVERT: Q 1242 ILE cc_start: 0.7708 (mm) cc_final: 0.7470 (mt) REVERT: Q 1260 LYS cc_start: 0.8356 (mtpp) cc_final: 0.8083 (mtpp) REVERT: Q 1266 GLU cc_start: 0.7673 (mp0) cc_final: 0.7124 (mp0) REVERT: Q 1280 LYS cc_start: 0.8047 (ptpp) cc_final: 0.7713 (ptpp) REVERT: Q 1405 MET cc_start: 0.6745 (tmm) cc_final: 0.6492 (mmm) REVERT: Q 1432 MET cc_start: 0.4723 (tpp) cc_final: 0.4502 (tpp) REVERT: Z 314 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7776 (pp20) outliers start: 160 outliers final: 62 residues processed: 934 average time/residue: 1.6196 time to fit residues: 1727.3315 Evaluate side-chains 906 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 823 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 LYS Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 132 ASN Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 146 GLN Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 750 THR Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 236 GLU Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 239 VAL Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 331 LYS Chi-restraints excluded: chain U residue 336 ASN Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 161 LYS Chi-restraints excluded: chain V residue 322 THR Chi-restraints excluded: chain V residue 353 VAL Chi-restraints excluded: chain V residue 389 THR Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 398 SER Chi-restraints excluded: chain V residue 430 ASN Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 233 LYS Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 338 LYS Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 373 GLN Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 386 ARG Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain X residue 454 LYS Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 238 THR Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 440 VAL Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1035 THR Chi-restraints excluded: chain Q residue 1103 ASP Chi-restraints excluded: chain Q residue 1161 ASN Chi-restraints excluded: chain Q residue 1199 GLU Chi-restraints excluded: chain Q residue 1233 ILE Chi-restraints excluded: chain Z residue 314 GLU Chi-restraints excluded: chain Z residue 315 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 0.0770 chunk 246 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 220 optimal weight: 0.6980 chunk 329 optimal weight: 0.6980 chunk 348 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 312 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 65 ASN R 107 ASN R 610 HIS R 633 GLN ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 360 ASN U 362 GLN U 407 GLN U 441 GLN U 446 GLN U 455 GLN V 51 GLN V 263 GLN V 314 ASN V 394 GLN V 417 GLN ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 173 ASN X 256 ASN X 271 GLN X 289 ASN X 325 ASN Y 49 GLN Y 310 ASN Y 373 GLN Q1244 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29102 Z= 0.208 Angle : 0.561 9.188 39373 Z= 0.275 Chirality : 0.043 0.181 4620 Planarity : 0.003 0.047 5040 Dihedral : 6.947 130.960 4004 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.14 % Allowed : 27.08 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3618 helix: 0.67 (0.14), residues: 1505 sheet: 0.49 (0.20), residues: 645 loop : -1.01 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 280 HIS 0.006 0.001 HIS V 165 PHE 0.021 0.001 PHE R 691 TYR 0.017 0.001 TYR V 462 ARG 0.007 0.000 ARG T 431 *********************** 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 964 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 833 time to evaluate : 3.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.7861 (p0) cc_final: 0.7180 (p0) REVERT: R 38 SER cc_start: 0.8014 (t) cc_final: 0.7598 (m) REVERT: R 69 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7669 (mtpt) REVERT: R 70 PHE cc_start: 0.7017 (t80) cc_final: 0.6713 (t80) REVERT: R 74 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8364 (pptt) REVERT: R 95 GLN cc_start: 0.8327 (mt0) cc_final: 0.7798 (mt0) REVERT: R 121 HIS cc_start: 0.8405 (m90) cc_final: 0.8054 (m-70) REVERT: R 193 ASP cc_start: 0.7318 (p0) cc_final: 0.7039 (p0) REVERT: R 249 ASP cc_start: 0.7636 (m-30) cc_final: 0.7125 (m-30) REVERT: R 266 THR cc_start: 0.6603 (m) cc_final: 0.6268 (m) REVERT: R 268 GLU cc_start: 0.7728 (pm20) cc_final: 0.7403 (pm20) REVERT: R 587 ARG cc_start: 0.8344 (tpp80) cc_final: 0.7918 (tpp80) REVERT: R 609 GLN cc_start: 0.7846 (mt0) cc_final: 0.7530 (mt0) REVERT: R 617 GLU cc_start: 0.8126 (mp0) cc_final: 0.7732 (mp0) REVERT: R 623 GLU cc_start: 0.8138 (tp30) cc_final: 0.7351 (tm-30) REVERT: R 643 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7502 (tm-30) REVERT: R 647 LEU cc_start: 0.7882 (mp) cc_final: 0.7620 (mm) REVERT: R 659 GLN cc_start: 0.7254 (mm-40) cc_final: 0.6906 (mm-40) REVERT: R 705 ASP cc_start: 0.7287 (t0) cc_final: 0.7036 (t0) REVERT: R 719 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6808 (mpp80) REVERT: R 733 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6957 (mp0) REVERT: R 743 LYS cc_start: 0.7623 (tptm) cc_final: 0.7015 (tttp) REVERT: R 744 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7986 (mt-10) REVERT: R 751 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7519 (ttpt) REVERT: S 77 LEU cc_start: 0.8177 (mp) cc_final: 0.7876 (mt) REVERT: S 80 LYS cc_start: 0.8409 (tmmt) cc_final: 0.8193 (tmmt) REVERT: S 141 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6911 (mm-40) REVERT: T 31 LYS cc_start: 0.8391 (mmtp) cc_final: 0.8004 (mmtt) REVERT: T 76 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7803 (tp) REVERT: T 141 GLU cc_start: 0.7932 (tp30) cc_final: 0.7535 (tp30) REVERT: T 146 GLU cc_start: 0.7751 (tt0) cc_final: 0.7550 (tt0) REVERT: T 205 ASN cc_start: 0.7426 (m-40) cc_final: 0.7003 (m-40) REVERT: T 206 THR cc_start: 0.7796 (m) cc_final: 0.7138 (p) REVERT: T 234 LYS cc_start: 0.8355 (mmmm) cc_final: 0.7812 (mmmm) REVERT: T 279 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7436 (mt-10) REVERT: T 282 GLU cc_start: 0.7193 (pm20) cc_final: 0.6884 (pm20) REVERT: T 294 LYS cc_start: 0.7879 (ttmm) cc_final: 0.7676 (ttpt) REVERT: T 312 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7894 (mp0) REVERT: T 386 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.7420 (mpt180) REVERT: T 392 ARG cc_start: 0.7572 (mtm110) cc_final: 0.7112 (mtm-85) REVERT: T 393 LEU cc_start: 0.7663 (mt) cc_final: 0.7448 (mt) REVERT: T 413 ARG cc_start: 0.7093 (mtt180) cc_final: 0.6524 (mtt180) REVERT: T 441 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7344 (tt0) REVERT: U 32 ASP cc_start: 0.7595 (m-30) cc_final: 0.7305 (m-30) REVERT: U 71 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7900 (p) REVERT: U 105 GLU cc_start: 0.7890 (tt0) cc_final: 0.7586 (mt-10) REVERT: U 110 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6906 (pp20) REVERT: U 125 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8107 (mt) REVERT: U 127 ILE cc_start: 0.8541 (mt) cc_final: 0.8338 (mp) REVERT: U 142 GLU cc_start: 0.7526 (tt0) cc_final: 0.7009 (tm-30) REVERT: U 155 GLN cc_start: 0.7173 (mt0) cc_final: 0.6935 (mt0) REVERT: U 164 ASP cc_start: 0.8071 (m-30) cc_final: 0.7699 (m-30) REVERT: U 170 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7411 (tp30) REVERT: U 174 LYS cc_start: 0.7467 (mtpt) cc_final: 0.7258 (mtpt) REVERT: U 237 HIS cc_start: 0.8223 (m-70) cc_final: 0.7910 (m-70) REVERT: U 255 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7552 (mp) REVERT: U 271 ASP cc_start: 0.7135 (m-30) cc_final: 0.6772 (m-30) REVERT: U 282 GLU cc_start: 0.7755 (tp30) cc_final: 0.7434 (tp30) REVERT: U 297 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8044 (mp0) REVERT: U 350 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7053 (mtp85) REVERT: U 362 GLN cc_start: 0.6730 (tp40) cc_final: 0.6475 (mm-40) REVERT: U 374 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7194 (mm-30) REVERT: U 407 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7852 (tp40) REVERT: U 451 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7650 (mp10) REVERT: V 36 ASP cc_start: 0.7563 (m-30) cc_final: 0.7161 (p0) REVERT: V 42 LYS cc_start: 0.7743 (mtmm) cc_final: 0.7038 (tttm) REVERT: V 111 TYR cc_start: 0.8336 (m-80) cc_final: 0.8034 (m-80) REVERT: V 122 MET cc_start: 0.8000 (tpp) cc_final: 0.7746 (tpp) REVERT: V 135 GLU cc_start: 0.7786 (tt0) cc_final: 0.7365 (tt0) REVERT: V 144 VAL cc_start: 0.8139 (t) cc_final: 0.7845 (m) REVERT: V 148 THR cc_start: 0.8078 (m) cc_final: 0.7480 (p) REVERT: V 154 ASN cc_start: 0.7548 (t0) cc_final: 0.7168 (t0) REVERT: V 161 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8307 (ttmm) REVERT: V 203 GLU cc_start: 0.8070 (tt0) cc_final: 0.7656 (tt0) REVERT: V 214 ARG cc_start: 0.7502 (mmt180) cc_final: 0.7120 (mmp-170) REVERT: V 216 ASP cc_start: 0.7099 (p0) cc_final: 0.6793 (p0) REVERT: V 221 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6894 (tm-30) REVERT: V 236 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7602 (mm-30) REVERT: V 256 ASN cc_start: 0.8370 (m-40) cc_final: 0.8166 (m-40) REVERT: V 268 MET cc_start: 0.7607 (mmm) cc_final: 0.7257 (mmm) REVERT: V 269 MET cc_start: 0.8037 (mmp) cc_final: 0.7738 (mmm) REVERT: V 287 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7515 (mm-30) REVERT: V 290 LYS cc_start: 0.7604 (mtpp) cc_final: 0.7400 (mtpm) REVERT: V 311 ASP cc_start: 0.7930 (t0) cc_final: 0.7606 (t0) REVERT: V 317 ASP cc_start: 0.7897 (m-30) cc_final: 0.7330 (m-30) REVERT: V 354 ILE cc_start: 0.7794 (mt) cc_final: 0.7528 (mm) REVERT: V 376 ASP cc_start: 0.7235 (m-30) cc_final: 0.6972 (m-30) REVERT: V 385 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7112 (mm-30) REVERT: V 389 THR cc_start: 0.7957 (OUTLIER) cc_final: 0.7734 (t) REVERT: V 428 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8184 (t) REVERT: V 443 LYS cc_start: 0.7758 (mtpp) cc_final: 0.7515 (mtpp) REVERT: W 36 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7306 (mm-40) REVERT: W 130 LYS cc_start: 0.7995 (ttmm) cc_final: 0.7691 (ttpp) REVERT: W 181 LYS cc_start: 0.7716 (ttpp) cc_final: 0.7511 (ttmt) REVERT: W 182 GLU cc_start: 0.7510 (tp30) cc_final: 0.7186 (tp30) REVERT: W 198 LYS cc_start: 0.8337 (tttt) cc_final: 0.8109 (tttt) REVERT: W 220 ARG cc_start: 0.7044 (mpp80) cc_final: 0.6810 (mpp80) REVERT: W 283 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6263 (tm-30) REVERT: W 285 LYS cc_start: 0.8089 (ttmm) cc_final: 0.7557 (ttpp) REVERT: W 338 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8200 (mttm) REVERT: W 381 SER cc_start: 0.7385 (m) cc_final: 0.7058 (p) REVERT: W 385 ASP cc_start: 0.7235 (m-30) cc_final: 0.6847 (m-30) REVERT: W 389 LYS cc_start: 0.7623 (mmmm) cc_final: 0.7251 (mmmm) REVERT: W 393 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6358 (mt-10) REVERT: W 419 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6923 (mm-30) REVERT: W 425 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7355 (ttt90) REVERT: W 455 GLN cc_start: 0.7346 (mm110) cc_final: 0.7071 (tt0) REVERT: X 37 GLU cc_start: 0.7695 (pp20) cc_final: 0.7317 (pp20) REVERT: X 94 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6570 (mt0) REVERT: X 125 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7483 (t80) REVERT: X 134 LYS cc_start: 0.8095 (ptpt) cc_final: 0.7704 (ptpp) REVERT: X 135 GLU cc_start: 0.7247 (tt0) cc_final: 0.6637 (mt-10) REVERT: X 143 GLU cc_start: 0.7709 (tt0) cc_final: 0.7189 (tt0) REVERT: X 150 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7075 (tt0) REVERT: X 156 LEU cc_start: 0.8710 (mt) cc_final: 0.8476 (mp) REVERT: X 177 LYS cc_start: 0.8268 (ttmt) cc_final: 0.7870 (ttmm) REVERT: X 180 ARG cc_start: 0.7793 (mtp180) cc_final: 0.7538 (mtp180) REVERT: X 182 ASP cc_start: 0.8163 (t70) cc_final: 0.7543 (t0) REVERT: X 196 ILE cc_start: 0.8130 (mt) cc_final: 0.7873 (mp) REVERT: X 221 GLU cc_start: 0.7696 (tp30) cc_final: 0.7258 (tt0) REVERT: X 229 TYR cc_start: 0.7578 (m-80) cc_final: 0.7153 (m-80) REVERT: X 242 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7454 (mp0) REVERT: X 243 ILE cc_start: 0.7756 (mt) cc_final: 0.7462 (OUTLIER) REVERT: X 282 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6836 (tm-30) REVERT: X 317 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6847 (m-30) REVERT: X 341 ASN cc_start: 0.8554 (p0) cc_final: 0.8158 (p0) REVERT: X 351 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6948 (mm-30) REVERT: Y 26 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8212 (mp) REVERT: Y 69 ARG cc_start: 0.8104 (mtt90) cc_final: 0.7763 (mmm-85) REVERT: Y 106 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7897 (mp) REVERT: Y 129 ILE cc_start: 0.8194 (mm) cc_final: 0.7989 (mm) REVERT: Y 130 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7928 (ttpp) REVERT: Y 236 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8169 (t) REVERT: Y 282 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7410 (tp30) REVERT: Y 297 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7768 (mm-30) REVERT: Y 317 PHE cc_start: 0.8481 (m-80) cc_final: 0.8058 (m-80) REVERT: Y 327 ARG cc_start: 0.8383 (mmt-90) cc_final: 0.8181 (mmt-90) REVERT: Y 331 LYS cc_start: 0.8097 (ttpt) cc_final: 0.7803 (ttpt) REVERT: Y 350 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7155 (mtp85) REVERT: Y 357 LYS cc_start: 0.8418 (mttm) cc_final: 0.7877 (mmmm) REVERT: Y 378 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7167 (mt-10) REVERT: Q 1021 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: Q 1078 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7303 (mtm-85) REVERT: Q 1092 ASP cc_start: 0.7556 (m-30) cc_final: 0.7236 (m-30) REVERT: Q 1103 ASP cc_start: 0.7694 (p0) cc_final: 0.6992 (p0) REVERT: Q 1123 GLU cc_start: 0.7637 (mp0) cc_final: 0.7303 (mp0) REVERT: Q 1134 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7529 (mm-30) REVERT: Q 1160 LYS cc_start: 0.7756 (ptpp) cc_final: 0.7401 (ptpp) REVERT: Q 1176 GLU cc_start: 0.7249 (mm-30) cc_final: 0.7009 (mm-30) REVERT: Q 1189 SER cc_start: 0.7964 (t) cc_final: 0.7594 (p) REVERT: Q 1200 ARG cc_start: 0.7656 (mtm110) cc_final: 0.7277 (mtp85) REVERT: Q 1231 ASN cc_start: 0.7825 (m-40) cc_final: 0.7545 (m-40) REVERT: Q 1239 ASP cc_start: 0.7139 (t0) cc_final: 0.6870 (t70) REVERT: Q 1242 ILE cc_start: 0.7746 (mm) cc_final: 0.7519 (mt) REVERT: Q 1260 LYS cc_start: 0.8342 (mtpp) cc_final: 0.8074 (mtpp) REVERT: Q 1266 GLU cc_start: 0.7683 (mp0) cc_final: 0.7129 (mp0) REVERT: Q 1270 LYS cc_start: 0.7425 (ptpt) cc_final: 0.7199 (ptpt) REVERT: Q 1280 LYS cc_start: 0.8045 (ptpp) cc_final: 0.7710 (ptpp) REVERT: Q 1301 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6920 (tt) REVERT: Q 1305 ASP cc_start: 0.7859 (m-30) cc_final: 0.7464 (m-30) REVERT: Q 1405 MET cc_start: 0.6828 (tmm) cc_final: 0.6593 (mmm) REVERT: Z 314 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7807 (pp20) outliers start: 131 outliers final: 59 residues processed: 890 average time/residue: 1.6510 time to fit residues: 1676.1321 Evaluate side-chains 905 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 822 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 LYS Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 132 ASN Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain R residue 750 THR Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 147 MET Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 253 ASP Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 398 SER Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 346 ASP Chi-restraints excluded: chain U residue 350 ARG Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 407 GLN Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 161 LYS Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 389 THR Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 398 SER Chi-restraints excluded: chain V residue 400 LEU Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 233 LYS Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 336 ASN Chi-restraints excluded: chain W residue 338 LYS Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 373 GLN Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 386 ARG Chi-restraints excluded: chain X residue 454 LYS Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 183 LYS Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 238 THR Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Q residue 950 ILE Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1035 THR Chi-restraints excluded: chain Q residue 1091 GLU Chi-restraints excluded: chain Q residue 1161 ASN Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1301 LEU Chi-restraints excluded: chain Z residue 314 GLU Chi-restraints excluded: chain Z residue 315 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 259 optimal weight: 0.0770 chunk 143 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 313 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 146 GLN R 610 HIS R 633 GLN ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 GLN V 263 GLN V 394 GLN V 417 GLN ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 173 ASN W 360 ASN X 271 GLN X 289 ASN X 325 ASN Y 310 ASN Q1244 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29102 Z= 0.239 Angle : 0.566 10.166 39373 Z= 0.277 Chirality : 0.043 0.201 4620 Planarity : 0.003 0.043 5040 Dihedral : 6.769 128.886 4004 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.71 % Allowed : 26.73 % Favored : 68.55 % 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: 0.04 (0.14), residues: 3618 helix: 0.81 (0.14), residues: 1507 sheet: 0.47 (0.20), residues: 651 loop : -0.94 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 280 HIS 0.005 0.001 HIS V 165 PHE 0.021 0.001 PHE R 691 TYR 0.026 0.001 TYR R 724 ARG 0.007 0.000 ARG T 431 *********************** 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 986 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 837 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.7851 (p0) cc_final: 0.7183 (p0) REVERT: R 38 SER cc_start: 0.8010 (t) cc_final: 0.7601 (m) REVERT: R 69 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7678 (mtpt) REVERT: R 70 PHE cc_start: 0.7023 (t80) cc_final: 0.6688 (t80) REVERT: R 74 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8375 (pptt) REVERT: R 121 HIS cc_start: 0.8433 (m90) cc_final: 0.8098 (m-70) REVERT: R 193 ASP cc_start: 0.7303 (p0) cc_final: 0.7028 (p0) REVERT: R 249 ASP cc_start: 0.7630 (m-30) cc_final: 0.7112 (m-30) REVERT: R 266 THR cc_start: 0.6636 (OUTLIER) cc_final: 0.6287 (m) REVERT: R 268 GLU cc_start: 0.7741 (pm20) cc_final: 0.7379 (pm20) REVERT: R 587 ARG cc_start: 0.8353 (tpp80) cc_final: 0.7879 (tpp80) REVERT: R 609 GLN cc_start: 0.7847 (mt0) cc_final: 0.7536 (mt0) REVERT: R 617 GLU cc_start: 0.8111 (mp0) cc_final: 0.7772 (mp0) REVERT: R 623 GLU cc_start: 0.8137 (tp30) cc_final: 0.7360 (tm-30) REVERT: R 643 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7495 (tm-30) REVERT: R 647 LEU cc_start: 0.7944 (mp) cc_final: 0.7675 (mm) REVERT: R 659 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6912 (mm-40) REVERT: R 705 ASP cc_start: 0.7301 (t0) cc_final: 0.7032 (t0) REVERT: R 719 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6856 (mpp80) REVERT: R 733 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6929 (mp0) REVERT: R 743 LYS cc_start: 0.7637 (tptm) cc_final: 0.6980 (ttmp) REVERT: R 744 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7971 (mt-10) REVERT: S 77 LEU cc_start: 0.8205 (mp) cc_final: 0.7795 (mp) REVERT: S 80 LYS cc_start: 0.8420 (tmmt) cc_final: 0.8219 (tmmt) REVERT: S 159 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7672 (ptm160) REVERT: T 31 LYS cc_start: 0.8388 (mmtp) cc_final: 0.8000 (mmtt) REVERT: T 76 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7836 (tp) REVERT: T 141 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7540 (tp30) REVERT: T 205 ASN cc_start: 0.7438 (m-40) cc_final: 0.7038 (m-40) REVERT: T 206 THR cc_start: 0.7783 (m) cc_final: 0.7312 (p) REVERT: T 234 LYS cc_start: 0.8339 (mmmm) cc_final: 0.7778 (mmmm) REVERT: T 282 GLU cc_start: 0.7180 (pm20) cc_final: 0.6862 (pm20) REVERT: T 312 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7877 (mp0) REVERT: T 332 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7324 (tp) REVERT: T 386 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7443 (mpt180) REVERT: T 392 ARG cc_start: 0.7556 (mtm110) cc_final: 0.7001 (mtm-85) REVERT: T 393 LEU cc_start: 0.7637 (mt) cc_final: 0.7414 (mt) REVERT: T 413 ARG cc_start: 0.7102 (mtt180) cc_final: 0.6574 (mtt180) REVERT: U 32 ASP cc_start: 0.7631 (m-30) cc_final: 0.7315 (m-30) REVERT: U 71 VAL cc_start: 0.8199 (OUTLIER) cc_final: 0.7903 (p) REVERT: U 105 GLU cc_start: 0.7899 (tt0) cc_final: 0.7583 (mt-10) REVERT: U 110 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6798 (pp20) REVERT: U 125 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8106 (mt) REVERT: U 127 ILE cc_start: 0.8538 (mt) cc_final: 0.8333 (mp) REVERT: U 134 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7308 (tp30) REVERT: U 142 GLU cc_start: 0.7486 (tt0) cc_final: 0.7000 (tm-30) REVERT: U 143 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7268 (mt) REVERT: U 155 GLN cc_start: 0.7160 (mt0) cc_final: 0.6926 (mt0) REVERT: U 170 GLU cc_start: 0.7836 (tt0) cc_final: 0.7434 (tp30) REVERT: U 174 LYS cc_start: 0.7501 (mtpt) cc_final: 0.7276 (mtpt) REVERT: U 237 HIS cc_start: 0.8246 (m-70) cc_final: 0.7929 (m-70) REVERT: U 255 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7561 (mp) REVERT: U 271 ASP cc_start: 0.7137 (m-30) cc_final: 0.6751 (m-30) REVERT: U 282 GLU cc_start: 0.7760 (tp30) cc_final: 0.7414 (tp30) REVERT: U 297 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8032 (mp0) REVERT: U 300 MET cc_start: 0.8681 (mmm) cc_final: 0.8318 (mmm) REVERT: U 350 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7043 (mtp85) REVERT: U 362 GLN cc_start: 0.6768 (tp40) cc_final: 0.6483 (mm-40) REVERT: U 374 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7175 (mm-30) REVERT: U 393 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: U 451 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7659 (mp10) REVERT: V 36 ASP cc_start: 0.7527 (m-30) cc_final: 0.7143 (p0) REVERT: V 42 LYS cc_start: 0.7751 (mtmm) cc_final: 0.6974 (tttm) REVERT: V 69 LYS cc_start: 0.7926 (ttmm) cc_final: 0.7610 (ttmm) REVERT: V 111 TYR cc_start: 0.8309 (m-80) cc_final: 0.8018 (m-80) REVERT: V 122 MET cc_start: 0.8026 (tpp) cc_final: 0.7766 (tpp) REVERT: V 135 GLU cc_start: 0.7786 (tt0) cc_final: 0.7387 (tt0) REVERT: V 144 VAL cc_start: 0.8150 (t) cc_final: 0.7866 (m) REVERT: V 148 THR cc_start: 0.8089 (m) cc_final: 0.7502 (p) REVERT: V 154 ASN cc_start: 0.7567 (t0) cc_final: 0.7191 (t0) REVERT: V 203 GLU cc_start: 0.8100 (tt0) cc_final: 0.7713 (tt0) REVERT: V 214 ARG cc_start: 0.7498 (mmt180) cc_final: 0.7078 (mmp-170) REVERT: V 216 ASP cc_start: 0.7103 (p0) cc_final: 0.6811 (p0) REVERT: V 221 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6850 (tm-30) REVERT: V 236 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7615 (mm-30) REVERT: V 268 MET cc_start: 0.7619 (mmm) cc_final: 0.7331 (mmm) REVERT: V 269 MET cc_start: 0.8010 (mmp) cc_final: 0.7722 (mmm) REVERT: V 287 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7543 (mm-30) REVERT: V 311 ASP cc_start: 0.7921 (t0) cc_final: 0.7601 (t0) REVERT: V 317 ASP cc_start: 0.7884 (m-30) cc_final: 0.7350 (m-30) REVERT: V 354 ILE cc_start: 0.7802 (mt) cc_final: 0.7525 (mm) REVERT: V 376 ASP cc_start: 0.7301 (m-30) cc_final: 0.7045 (m-30) REVERT: V 385 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7054 (mm-30) REVERT: V 389 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7746 (t) REVERT: V 428 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8173 (t) REVERT: V 443 LYS cc_start: 0.7803 (mtpp) cc_final: 0.7574 (mtpp) REVERT: W 36 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7327 (mm-40) REVERT: W 130 LYS cc_start: 0.7958 (ttmm) cc_final: 0.7660 (ttpp) REVERT: W 181 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7467 (ttmt) REVERT: W 182 GLU cc_start: 0.7512 (tp30) cc_final: 0.7181 (tp30) REVERT: W 198 LYS cc_start: 0.8343 (tttt) cc_final: 0.8119 (tttt) REVERT: W 283 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6446 (tm-30) REVERT: W 285 LYS cc_start: 0.8065 (ttmm) cc_final: 0.7436 (ttpp) REVERT: W 338 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8238 (mttm) REVERT: W 381 SER cc_start: 0.7418 (m) cc_final: 0.7071 (p) REVERT: W 385 ASP cc_start: 0.7219 (m-30) cc_final: 0.6825 (m-30) REVERT: W 389 LYS cc_start: 0.7597 (mmmm) cc_final: 0.7238 (mmmm) REVERT: W 393 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6362 (mt-10) REVERT: W 419 GLU cc_start: 0.7299 (mm-30) cc_final: 0.7010 (mm-30) REVERT: W 425 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7359 (ttt90) REVERT: W 455 GLN cc_start: 0.7333 (mm110) cc_final: 0.7060 (tt0) REVERT: X 37 GLU cc_start: 0.7708 (pp20) cc_final: 0.7300 (pp20) REVERT: X 94 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6617 (mp10) REVERT: X 125 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7490 (t80) REVERT: X 134 LYS cc_start: 0.8074 (ptpt) cc_final: 0.7694 (ptpp) REVERT: X 135 GLU cc_start: 0.7243 (tt0) cc_final: 0.6621 (mt-10) REVERT: X 143 GLU cc_start: 0.7701 (tt0) cc_final: 0.7182 (tt0) REVERT: X 150 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7101 (tt0) REVERT: X 156 LEU cc_start: 0.8711 (mt) cc_final: 0.8472 (mp) REVERT: X 177 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7875 (ttmm) REVERT: X 180 ARG cc_start: 0.7812 (mtp180) cc_final: 0.7545 (mtp180) REVERT: X 182 ASP cc_start: 0.8181 (t70) cc_final: 0.7685 (t0) REVERT: X 196 ILE cc_start: 0.8131 (mt) cc_final: 0.7883 (mp) REVERT: X 221 GLU cc_start: 0.7735 (tp30) cc_final: 0.7290 (tt0) REVERT: X 229 TYR cc_start: 0.7521 (m-80) cc_final: 0.6932 (m-80) REVERT: X 242 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7435 (mp0) REVERT: X 243 ILE cc_start: 0.7776 (mt) cc_final: 0.7487 (mp) REVERT: X 264 ASP cc_start: 0.7329 (p0) cc_final: 0.7061 (p0) REVERT: X 282 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6839 (tm-30) REVERT: X 317 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6859 (m-30) REVERT: X 341 ASN cc_start: 0.8540 (p0) cc_final: 0.8187 (p0) REVERT: X 351 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6977 (mm-30) REVERT: Y 26 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8193 (mp) REVERT: Y 69 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7768 (mmm-85) REVERT: Y 106 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7927 (mp) REVERT: Y 129 ILE cc_start: 0.8206 (mm) cc_final: 0.7996 (mm) REVERT: Y 130 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7927 (ttpp) REVERT: Y 176 ILE cc_start: 0.6368 (mm) cc_final: 0.6099 (mp) REVERT: Y 236 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8168 (t) REVERT: Y 272 GLN cc_start: 0.7254 (tt0) cc_final: 0.7032 (tt0) REVERT: Y 282 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7393 (mm-30) REVERT: Y 297 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7739 (mm-30) REVERT: Y 317 PHE cc_start: 0.8493 (m-80) cc_final: 0.8076 (m-80) REVERT: Y 327 ARG cc_start: 0.8379 (mmt-90) cc_final: 0.8179 (mmt-90) REVERT: Y 350 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7151 (mtp85) REVERT: Y 357 LYS cc_start: 0.8417 (mttm) cc_final: 0.8122 (mmmm) REVERT: Y 378 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7168 (mt-10) REVERT: Q 1021 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: Q 1078 ARG cc_start: 0.7733 (mtm-85) cc_final: 0.7278 (mtm-85) REVERT: Q 1092 ASP cc_start: 0.7556 (m-30) cc_final: 0.7224 (m-30) REVERT: Q 1112 LYS cc_start: 0.8252 (mtpp) cc_final: 0.8027 (mtmm) REVERT: Q 1123 GLU cc_start: 0.7657 (mp0) cc_final: 0.7317 (mp0) REVERT: Q 1134 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7533 (mm-30) REVERT: Q 1160 LYS cc_start: 0.7813 (ptpp) cc_final: 0.7465 (ptpp) REVERT: Q 1176 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6992 (mm-30) REVERT: Q 1189 SER cc_start: 0.7942 (t) cc_final: 0.7556 (p) REVERT: Q 1200 ARG cc_start: 0.7675 (mtm110) cc_final: 0.7284 (mtp85) REVERT: Q 1231 ASN cc_start: 0.7831 (m-40) cc_final: 0.7560 (m-40) REVERT: Q 1239 ASP cc_start: 0.7136 (t0) cc_final: 0.6775 (t70) REVERT: Q 1242 ILE cc_start: 0.7747 (mm) cc_final: 0.7461 (mt) REVERT: Q 1260 LYS cc_start: 0.8326 (mtpp) cc_final: 0.8061 (mtpp) REVERT: Q 1266 GLU cc_start: 0.7691 (mp0) cc_final: 0.7151 (mp0) REVERT: Q 1280 LYS cc_start: 0.8034 (ptpp) cc_final: 0.7699 (ptpp) REVERT: Q 1405 MET cc_start: 0.6853 (tmm) cc_final: 0.6541 (mmm) REVERT: Z 314 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7825 (pp20) outliers start: 149 outliers final: 80 residues processed: 907 average time/residue: 1.6379 time to fit residues: 1698.9544 Evaluate side-chains 931 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 822 time to evaluate : 3.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 LYS Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 132 ASN Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 591 LEU Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain R residue 750 THR Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 147 MET Chi-restraints excluded: chain S residue 159 ARG Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 253 ASP Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain T residue 398 SER Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 336 ASN Chi-restraints excluded: chain U residue 346 ASP Chi-restraints excluded: chain U residue 350 ARG Chi-restraints excluded: chain U residue 393 GLU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 389 THR Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 336 ASN Chi-restraints excluded: chain W residue 338 LYS Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 373 GLN Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain X residue 31 LYS Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 138 GLU Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 386 ARG Chi-restraints excluded: chain X residue 454 LYS Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 183 LYS Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 219 THR Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 238 THR Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Q residue 950 ILE Chi-restraints excluded: chain Q residue 1005 MET Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1035 THR Chi-restraints excluded: chain Q residue 1091 GLU Chi-restraints excluded: chain Q residue 1103 ASP Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1161 ASN Chi-restraints excluded: chain Q residue 1193 VAL Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1343 ILE Chi-restraints excluded: chain Z residue 314 GLU Chi-restraints excluded: chain Z residue 315 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 0.9990 chunk 314 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 204 optimal weight: 0.0070 chunk 86 optimal weight: 1.9990 chunk 349 optimal weight: 5.9990 chunk 289 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 65 ASN R 146 GLN R 610 HIS R 633 GLN ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 310 ASN V 51 GLN V 394 GLN V 417 GLN ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 173 ASN W 360 ASN X 124 ASN X 271 GLN X 289 ASN X 325 ASN Y 310 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29102 Z= 0.288 Angle : 0.582 8.648 39373 Z= 0.287 Chirality : 0.044 0.202 4620 Planarity : 0.004 0.040 5040 Dihedral : 6.739 126.365 4004 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.00 % Allowed : 27.24 % Favored : 67.76 % 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: 0.05 (0.14), residues: 3618 helix: 0.82 (0.14), residues: 1508 sheet: 0.54 (0.20), residues: 639 loop : -0.97 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 280 HIS 0.004 0.001 HIS T 165 PHE 0.022 0.001 PHE R 691 TYR 0.019 0.002 TYR V 462 ARG 0.008 0.000 ARG T 371 *********************** 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 996 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 838 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.7858 (p0) cc_final: 0.7217 (p0) REVERT: R 38 SER cc_start: 0.8010 (t) cc_final: 0.7620 (m) REVERT: R 69 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7680 (mtpt) REVERT: R 70 PHE cc_start: 0.6967 (t80) cc_final: 0.6625 (t80) REVERT: R 74 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8404 (pptt) REVERT: R 93 ARG cc_start: 0.8582 (ttm-80) cc_final: 0.7883 (ttm170) REVERT: R 121 HIS cc_start: 0.8440 (m90) cc_final: 0.8137 (m-70) REVERT: R 193 ASP cc_start: 0.7301 (p0) cc_final: 0.7021 (p0) REVERT: R 237 LYS cc_start: 0.7729 (mmpt) cc_final: 0.7523 (mmpt) REVERT: R 249 ASP cc_start: 0.7674 (m-30) cc_final: 0.7154 (m-30) REVERT: R 266 THR cc_start: 0.6660 (OUTLIER) cc_final: 0.6307 (m) REVERT: R 268 GLU cc_start: 0.7750 (pm20) cc_final: 0.7353 (pm20) REVERT: R 587 ARG cc_start: 0.8360 (tpp80) cc_final: 0.8115 (tpp80) REVERT: R 609 GLN cc_start: 0.7873 (mt0) cc_final: 0.7554 (mt0) REVERT: R 617 GLU cc_start: 0.8081 (mp0) cc_final: 0.7817 (mp0) REVERT: R 623 GLU cc_start: 0.8135 (tp30) cc_final: 0.7345 (tm-30) REVERT: R 643 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7489 (tm-30) REVERT: R 647 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7722 (mm) REVERT: R 659 GLN cc_start: 0.7259 (mm-40) cc_final: 0.6973 (mm-40) REVERT: R 705 ASP cc_start: 0.7328 (t0) cc_final: 0.7083 (t0) REVERT: R 719 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6804 (mpp80) REVERT: R 733 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6907 (mp0) REVERT: R 743 LYS cc_start: 0.7672 (tptm) cc_final: 0.6961 (ttmp) REVERT: R 744 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8025 (mt-10) REVERT: S 77 LEU cc_start: 0.8235 (mp) cc_final: 0.7813 (mp) REVERT: S 159 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7486 (ptm160) REVERT: T 31 LYS cc_start: 0.8406 (mmtp) cc_final: 0.8109 (mmtt) REVERT: T 76 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7879 (tp) REVERT: T 141 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7544 (tp30) REVERT: T 205 ASN cc_start: 0.7496 (m-40) cc_final: 0.7094 (m-40) REVERT: T 216 ASP cc_start: 0.8265 (t70) cc_final: 0.7841 (m-30) REVERT: T 234 LYS cc_start: 0.8345 (mmmm) cc_final: 0.7775 (mmmm) REVERT: T 282 GLU cc_start: 0.7144 (pm20) cc_final: 0.6807 (pm20) REVERT: T 312 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7860 (mp0) REVERT: T 332 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7330 (tp) REVERT: T 386 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7430 (mpt180) REVERT: T 392 ARG cc_start: 0.7558 (mtm110) cc_final: 0.7010 (mtm-85) REVERT: T 393 LEU cc_start: 0.7675 (mt) cc_final: 0.7444 (mt) REVERT: T 413 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6622 (mtt180) REVERT: U 32 ASP cc_start: 0.7623 (m-30) cc_final: 0.7322 (m-30) REVERT: U 71 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7890 (p) REVERT: U 125 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8145 (mt) REVERT: U 127 ILE cc_start: 0.8548 (mt) cc_final: 0.8343 (mp) REVERT: U 134 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7298 (tp30) REVERT: U 142 GLU cc_start: 0.7471 (tt0) cc_final: 0.7018 (tm-30) REVERT: U 143 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7249 (mt) REVERT: U 155 GLN cc_start: 0.7163 (mt0) cc_final: 0.6934 (mt0) REVERT: U 170 GLU cc_start: 0.7825 (tt0) cc_final: 0.7420 (tp30) REVERT: U 174 LYS cc_start: 0.7455 (mtpt) cc_final: 0.7213 (mtpt) REVERT: U 193 ASP cc_start: 0.8192 (t0) cc_final: 0.7624 (t0) REVERT: U 255 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7555 (mp) REVERT: U 271 ASP cc_start: 0.7132 (m-30) cc_final: 0.6908 (m-30) REVERT: U 282 GLU cc_start: 0.7760 (tp30) cc_final: 0.7406 (tp30) REVERT: U 297 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8049 (mp0) REVERT: U 300 MET cc_start: 0.8668 (mmm) cc_final: 0.8311 (mmm) REVERT: U 350 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7069 (mtp85) REVERT: U 362 GLN cc_start: 0.6807 (tp40) cc_final: 0.6511 (mm-40) REVERT: U 451 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7659 (mp10) REVERT: V 36 ASP cc_start: 0.7519 (m-30) cc_final: 0.7169 (p0) REVERT: V 42 LYS cc_start: 0.7733 (mtmm) cc_final: 0.6959 (tttm) REVERT: V 69 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7617 (ttmm) REVERT: V 109 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7190 (mp0) REVERT: V 111 TYR cc_start: 0.8290 (m-80) cc_final: 0.7998 (m-80) REVERT: V 135 GLU cc_start: 0.7809 (tt0) cc_final: 0.7381 (tt0) REVERT: V 148 THR cc_start: 0.8022 (m) cc_final: 0.7443 (p) REVERT: V 154 ASN cc_start: 0.7574 (t0) cc_final: 0.7211 (t0) REVERT: V 165 HIS cc_start: 0.7919 (m90) cc_final: 0.7635 (m90) REVERT: V 203 GLU cc_start: 0.8106 (tt0) cc_final: 0.7743 (tt0) REVERT: V 214 ARG cc_start: 0.7486 (mmt180) cc_final: 0.7017 (mmp-170) REVERT: V 216 ASP cc_start: 0.7142 (p0) cc_final: 0.6851 (p0) REVERT: V 221 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6865 (tm-30) REVERT: V 236 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7624 (mm-30) REVERT: V 287 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7599 (mm-30) REVERT: V 311 ASP cc_start: 0.7942 (t0) cc_final: 0.7606 (t0) REVERT: V 317 ASP cc_start: 0.7883 (m-30) cc_final: 0.7356 (m-30) REVERT: V 329 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7562 (tm-30) REVERT: V 354 ILE cc_start: 0.7816 (mt) cc_final: 0.7537 (mm) REVERT: V 376 ASP cc_start: 0.7479 (m-30) cc_final: 0.7208 (m-30) REVERT: V 385 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7163 (mm-30) REVERT: V 428 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8149 (t) REVERT: V 443 LYS cc_start: 0.7838 (mtpp) cc_final: 0.7631 (mtpp) REVERT: W 36 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7232 (mm110) REVERT: W 130 LYS cc_start: 0.7954 (ttmm) cc_final: 0.7666 (ttpp) REVERT: W 142 GLU cc_start: 0.8140 (tt0) cc_final: 0.7870 (tt0) REVERT: W 181 LYS cc_start: 0.7682 (ttpp) cc_final: 0.7433 (ttmt) REVERT: W 182 GLU cc_start: 0.7494 (tp30) cc_final: 0.7014 (tm-30) REVERT: W 198 LYS cc_start: 0.8343 (tttt) cc_final: 0.8098 (tttt) REVERT: W 226 GLU cc_start: 0.7090 (mp0) cc_final: 0.6632 (mp0) REVERT: W 228 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7854 (mm-30) REVERT: W 283 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6896 (tm-30) REVERT: W 285 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7779 (ttpp) REVERT: W 338 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8252 (mttm) REVERT: W 374 GLU cc_start: 0.7119 (tp30) cc_final: 0.6644 (tp30) REVERT: W 381 SER cc_start: 0.7450 (m) cc_final: 0.7086 (p) REVERT: W 385 ASP cc_start: 0.7220 (m-30) cc_final: 0.6828 (m-30) REVERT: W 389 LYS cc_start: 0.7587 (mmmm) cc_final: 0.7265 (mmmm) REVERT: W 393 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6490 (mt-10) REVERT: W 419 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6658 (mp0) REVERT: W 425 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7344 (ttt90) REVERT: W 455 GLN cc_start: 0.7328 (mm110) cc_final: 0.7060 (tt0) REVERT: X 37 GLU cc_start: 0.7700 (pp20) cc_final: 0.7334 (pp20) REVERT: X 94 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.6648 (mp10) REVERT: X 105 LEU cc_start: 0.8339 (tp) cc_final: 0.8112 (tp) REVERT: X 125 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7483 (t80) REVERT: X 134 LYS cc_start: 0.8066 (ptpt) cc_final: 0.7697 (ptpp) REVERT: X 135 GLU cc_start: 0.7224 (tt0) cc_final: 0.6617 (mt-10) REVERT: X 143 GLU cc_start: 0.7717 (tt0) cc_final: 0.7192 (tt0) REVERT: X 150 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7121 (tt0) REVERT: X 156 LEU cc_start: 0.8711 (mt) cc_final: 0.8482 (OUTLIER) REVERT: X 177 LYS cc_start: 0.8282 (ttmt) cc_final: 0.7810 (ttmm) REVERT: X 182 ASP cc_start: 0.8169 (t70) cc_final: 0.7502 (t0) REVERT: X 196 ILE cc_start: 0.8102 (mt) cc_final: 0.7862 (mp) REVERT: X 221 GLU cc_start: 0.7778 (tp30) cc_final: 0.7312 (tt0) REVERT: X 229 TYR cc_start: 0.7475 (m-80) cc_final: 0.7047 (m-80) REVERT: X 232 LEU cc_start: 0.8757 (tp) cc_final: 0.8418 (mm) REVERT: X 242 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7411 (mp0) REVERT: X 243 ILE cc_start: 0.7748 (mt) cc_final: 0.7463 (mp) REVERT: X 264 ASP cc_start: 0.7314 (p0) cc_final: 0.7073 (p0) REVERT: X 282 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6840 (tm-30) REVERT: X 317 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6876 (m-30) REVERT: X 341 ASN cc_start: 0.8529 (p0) cc_final: 0.8193 (p0) REVERT: X 351 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6983 (mm-30) REVERT: Y 26 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8182 (mp) REVERT: Y 69 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7687 (mmt90) REVERT: Y 106 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7968 (mp) REVERT: Y 129 ILE cc_start: 0.8214 (mm) cc_final: 0.8006 (mm) REVERT: Y 130 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7932 (ttpp) REVERT: Y 176 ILE cc_start: 0.6404 (mm) cc_final: 0.6133 (mp) REVERT: Y 236 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8147 (t) REVERT: Y 272 GLN cc_start: 0.7259 (tt0) cc_final: 0.6976 (tt0) REVERT: Y 282 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7394 (mm-30) REVERT: Y 297 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7751 (mm-30) REVERT: Y 317 PHE cc_start: 0.8493 (m-80) cc_final: 0.8074 (m-80) REVERT: Y 350 ARG cc_start: 0.7696 (mtm-85) cc_final: 0.7166 (mtp85) REVERT: Y 357 LYS cc_start: 0.8413 (mttm) cc_final: 0.7923 (mmmm) REVERT: Y 378 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7176 (mt-10) REVERT: Q 1021 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: Q 1030 THR cc_start: 0.7996 (p) cc_final: 0.7394 (p) REVERT: Q 1078 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7330 (mtm-85) REVERT: Q 1087 ARG cc_start: 0.7768 (mtm110) cc_final: 0.7550 (mtm-85) REVERT: Q 1092 ASP cc_start: 0.7548 (m-30) cc_final: 0.7175 (m-30) REVERT: Q 1103 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7011 (p0) REVERT: Q 1123 GLU cc_start: 0.7651 (mp0) cc_final: 0.7311 (mp0) REVERT: Q 1134 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7513 (mm-30) REVERT: Q 1160 LYS cc_start: 0.7827 (ptpp) cc_final: 0.7473 (ptpp) REVERT: Q 1176 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6880 (mm-30) REVERT: Q 1189 SER cc_start: 0.7934 (t) cc_final: 0.7525 (p) REVERT: Q 1200 ARG cc_start: 0.7686 (mtm110) cc_final: 0.7268 (mtp85) REVERT: Q 1231 ASN cc_start: 0.7833 (m-40) cc_final: 0.7570 (m-40) REVERT: Q 1239 ASP cc_start: 0.7138 (t0) cc_final: 0.6875 (t70) REVERT: Q 1241 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7362 (tt) REVERT: Q 1242 ILE cc_start: 0.7764 (mm) cc_final: 0.7511 (mt) REVERT: Q 1260 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8087 (mtpp) REVERT: Q 1266 GLU cc_start: 0.7688 (mp0) cc_final: 0.7152 (mp0) REVERT: Q 1280 LYS cc_start: 0.8017 (ptpp) cc_final: 0.7688 (ptpp) REVERT: Q 1316 HIS cc_start: 0.8148 (m-70) cc_final: 0.7453 (m-70) REVERT: Q 1371 LEU cc_start: 0.7421 (mp) cc_final: 0.7048 (pt) REVERT: Q 1405 MET cc_start: 0.6870 (tmm) cc_final: 0.6544 (mmm) outliers start: 158 outliers final: 89 residues processed: 910 average time/residue: 1.6687 time to fit residues: 1741.0783 Evaluate side-chains 941 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 825 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 69 LYS Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 132 ASN Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 591 LEU Chi-restraints excluded: chain R residue 647 LEU Chi-restraints excluded: chain R residue 648 LYS Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain R residue 750 THR Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 147 MET Chi-restraints excluded: chain S residue 159 ARG Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 146 GLU Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 253 ASP Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain T residue 398 SER Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 239 VAL Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 281 LYS Chi-restraints excluded: chain U residue 346 ASP Chi-restraints excluded: chain U residue 350 ARG Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 322 THR Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 353 VAL Chi-restraints excluded: chain V residue 389 THR Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 398 SER Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 131 GLU Chi-restraints excluded: chain W residue 233 LYS Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 336 ASN Chi-restraints excluded: chain W residue 338 LYS Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 373 GLN Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain X residue 31 LYS Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 138 GLU Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 241 LYS Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 454 LYS Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 183 LYS Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 219 THR Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 238 THR Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Q residue 950 ILE Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1035 THR Chi-restraints excluded: chain Q residue 1091 GLU Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1103 ASP Chi-restraints excluded: chain Q residue 1193 VAL Chi-restraints excluded: chain Q residue 1241 LEU Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1324 MET Chi-restraints excluded: chain Q residue 1343 ILE Chi-restraints excluded: chain Q residue 1389 VAL Chi-restraints excluded: chain Z residue 315 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 5.9990 chunk 39 optimal weight: 0.0050 chunk 199 optimal weight: 1.9990 chunk 255 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 294 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 347 optimal weight: 0.0270 chunk 217 optimal weight: 2.9990 chunk 212 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 overall best weight: 0.4252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN R 610 HIS R 633 GLN U 248 ASN U 310 ASN U 360 ASN V 51 GLN V 263 GLN V 394 GLN V 417 GLN ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 173 ASN W 360 ASN X 256 ASN X 271 GLN X 289 ASN X 325 ASN Y 310 ASN Y 373 GLN Q1244 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29102 Z= 0.174 Angle : 0.550 8.403 39373 Z= 0.268 Chirality : 0.042 0.229 4620 Planarity : 0.003 0.037 5040 Dihedral : 6.449 123.094 4004 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.99 % Allowed : 29.04 % Favored : 66.97 % 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: 0.23 (0.14), residues: 3618 helix: 1.01 (0.14), residues: 1502 sheet: 0.49 (0.20), residues: 651 loop : -0.85 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 280 HIS 0.003 0.001 HIS U 242 PHE 0.018 0.001 PHE R 691 TYR 0.030 0.001 TYR R 724 ARG 0.007 0.000 ARG T 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 833 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.7848 (p0) cc_final: 0.7190 (p0) REVERT: R 38 SER cc_start: 0.7984 (t) cc_final: 0.7592 (m) REVERT: R 70 PHE cc_start: 0.6948 (t80) cc_final: 0.6607 (t80) REVERT: R 74 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8376 (pptt) REVERT: R 121 HIS cc_start: 0.8447 (m90) cc_final: 0.8145 (m-70) REVERT: R 193 ASP cc_start: 0.7290 (p0) cc_final: 0.7001 (p0) REVERT: R 237 LYS cc_start: 0.7699 (mmpt) cc_final: 0.7493 (mmpt) REVERT: R 249 ASP cc_start: 0.7643 (m-30) cc_final: 0.7119 (m-30) REVERT: R 266 THR cc_start: 0.6643 (OUTLIER) cc_final: 0.6340 (m) REVERT: R 268 GLU cc_start: 0.7750 (pm20) cc_final: 0.7337 (pm20) REVERT: R 587 ARG cc_start: 0.8354 (tpp80) cc_final: 0.8097 (tpp80) REVERT: R 609 GLN cc_start: 0.7880 (mt0) cc_final: 0.7557 (mt0) REVERT: R 617 GLU cc_start: 0.8134 (mp0) cc_final: 0.7883 (mp0) REVERT: R 623 GLU cc_start: 0.8120 (tp30) cc_final: 0.7348 (tm-30) REVERT: R 643 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7457 (tm-30) REVERT: R 647 LEU cc_start: 0.7976 (mp) cc_final: 0.7703 (mm) REVERT: R 659 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6923 (mm-40) REVERT: R 705 ASP cc_start: 0.7332 (t0) cc_final: 0.7086 (t0) REVERT: R 719 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6798 (mpp80) REVERT: R 733 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6867 (mp0) REVERT: R 743 LYS cc_start: 0.7660 (tptm) cc_final: 0.6986 (ttmp) REVERT: S 141 GLN cc_start: 0.7176 (mm-40) cc_final: 0.6813 (mm-40) REVERT: T 31 LYS cc_start: 0.8380 (mmtp) cc_final: 0.7993 (mmtt) REVERT: T 141 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7555 (tp30) REVERT: T 205 ASN cc_start: 0.7511 (m-40) cc_final: 0.7079 (m-40) REVERT: T 206 THR cc_start: 0.7843 (m) cc_final: 0.7169 (p) REVERT: T 216 ASP cc_start: 0.8244 (t70) cc_final: 0.7819 (m-30) REVERT: T 282 GLU cc_start: 0.7138 (pm20) cc_final: 0.6812 (pm20) REVERT: T 312 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7866 (mp0) REVERT: T 386 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7445 (mpt180) REVERT: T 392 ARG cc_start: 0.7567 (mtm110) cc_final: 0.7018 (mtm-85) REVERT: T 393 LEU cc_start: 0.7660 (mt) cc_final: 0.7411 (mt) REVERT: T 398 SER cc_start: 0.7585 (OUTLIER) cc_final: 0.7273 (m) REVERT: T 413 ARG cc_start: 0.7052 (mtt180) cc_final: 0.6563 (mtt180) REVERT: U 32 ASP cc_start: 0.7582 (m-30) cc_final: 0.7285 (m-30) REVERT: U 127 ILE cc_start: 0.8554 (mt) cc_final: 0.8349 (mp) REVERT: U 134 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: U 142 GLU cc_start: 0.7509 (tt0) cc_final: 0.7032 (tm-30) REVERT: U 143 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7244 (mt) REVERT: U 155 GLN cc_start: 0.7148 (mt0) cc_final: 0.6924 (mt0) REVERT: U 170 GLU cc_start: 0.7840 (tt0) cc_final: 0.7433 (tp30) REVERT: U 174 LYS cc_start: 0.7451 (mtpt) cc_final: 0.7196 (mtpt) REVERT: U 237 HIS cc_start: 0.8261 (m-70) cc_final: 0.7968 (m-70) REVERT: U 255 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7536 (mp) REVERT: U 271 ASP cc_start: 0.7157 (m-30) cc_final: 0.6754 (m-30) REVERT: U 282 GLU cc_start: 0.7760 (tp30) cc_final: 0.7422 (tp30) REVERT: U 300 MET cc_start: 0.8637 (mmm) cc_final: 0.8257 (mmm) REVERT: U 350 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7789 (ptp90) REVERT: U 362 GLN cc_start: 0.6789 (tp40) cc_final: 0.6486 (mm-40) REVERT: U 451 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7668 (mp10) REVERT: V 36 ASP cc_start: 0.7506 (m-30) cc_final: 0.7165 (p0) REVERT: V 42 LYS cc_start: 0.7727 (mtmm) cc_final: 0.6924 (tttm) REVERT: V 68 LYS cc_start: 0.7898 (mttp) cc_final: 0.7641 (mtpp) REVERT: V 69 LYS cc_start: 0.7892 (ttmm) cc_final: 0.7630 (ttmm) REVERT: V 109 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7295 (mm-30) REVERT: V 111 TYR cc_start: 0.8262 (m-80) cc_final: 0.7955 (m-80) REVERT: V 135 GLU cc_start: 0.7808 (tt0) cc_final: 0.7390 (tt0) REVERT: V 148 THR cc_start: 0.8028 (m) cc_final: 0.7448 (p) REVERT: V 154 ASN cc_start: 0.7588 (t0) cc_final: 0.7203 (t0) REVERT: V 168 VAL cc_start: 0.8110 (p) cc_final: 0.7856 (t) REVERT: V 203 GLU cc_start: 0.8069 (tt0) cc_final: 0.7712 (tt0) REVERT: V 214 ARG cc_start: 0.7450 (mmt180) cc_final: 0.7084 (mmp-170) REVERT: V 216 ASP cc_start: 0.7121 (p0) cc_final: 0.6834 (p0) REVERT: V 221 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6846 (tm-30) REVERT: V 236 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7609 (mm-30) REVERT: V 269 MET cc_start: 0.7929 (mmp) cc_final: 0.7639 (mmm) REVERT: V 287 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7573 (mm-30) REVERT: V 311 ASP cc_start: 0.7927 (t0) cc_final: 0.7441 (t0) REVERT: V 317 ASP cc_start: 0.7857 (m-30) cc_final: 0.7298 (m-30) REVERT: V 329 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7554 (tm-30) REVERT: V 354 ILE cc_start: 0.7813 (mt) cc_final: 0.7530 (mm) REVERT: V 376 ASP cc_start: 0.7416 (m-30) cc_final: 0.7181 (m-30) REVERT: V 385 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7123 (mm-30) REVERT: V 389 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7719 (t) REVERT: V 394 GLN cc_start: 0.7450 (pt0) cc_final: 0.6989 (pt0) REVERT: V 443 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7579 (mtpp) REVERT: W 36 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7215 (mm110) REVERT: W 130 LYS cc_start: 0.7933 (ttmm) cc_final: 0.7732 (ttpp) REVERT: W 142 GLU cc_start: 0.8125 (tt0) cc_final: 0.7851 (tt0) REVERT: W 181 LYS cc_start: 0.7714 (ttpp) cc_final: 0.7463 (ttmt) REVERT: W 182 GLU cc_start: 0.7482 (tp30) cc_final: 0.7066 (tm-30) REVERT: W 198 LYS cc_start: 0.8345 (tttt) cc_final: 0.8109 (tttt) REVERT: W 220 ARG cc_start: 0.7149 (mpp80) cc_final: 0.6880 (mpp80) REVERT: W 228 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7858 (mm-30) REVERT: W 283 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6830 (tm-30) REVERT: W 285 LYS cc_start: 0.8059 (ttmm) cc_final: 0.7788 (ttpp) REVERT: W 374 GLU cc_start: 0.7066 (tp30) cc_final: 0.6608 (tp30) REVERT: W 381 SER cc_start: 0.7407 (m) cc_final: 0.7020 (p) REVERT: W 385 ASP cc_start: 0.7237 (m-30) cc_final: 0.6826 (m-30) REVERT: W 389 LYS cc_start: 0.7583 (mmmm) cc_final: 0.7243 (mmmm) REVERT: W 393 GLU cc_start: 0.6688 (mt-10) cc_final: 0.6382 (mt-10) REVERT: W 419 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6440 (mp0) REVERT: W 425 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7313 (ttt90) REVERT: W 455 GLN cc_start: 0.7320 (mm110) cc_final: 0.7032 (tt0) REVERT: X 37 GLU cc_start: 0.7693 (pp20) cc_final: 0.7318 (pp20) REVERT: X 94 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6574 (mt0) REVERT: X 125 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7460 (t80) REVERT: X 134 LYS cc_start: 0.8063 (ptpt) cc_final: 0.7702 (ptpp) REVERT: X 135 GLU cc_start: 0.7221 (tt0) cc_final: 0.6614 (mt-10) REVERT: X 143 GLU cc_start: 0.7653 (tt0) cc_final: 0.7122 (tt0) REVERT: X 150 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7113 (tt0) REVERT: X 156 LEU cc_start: 0.8679 (mt) cc_final: 0.8444 (OUTLIER) REVERT: X 177 LYS cc_start: 0.8273 (ttmt) cc_final: 0.7804 (ttmm) REVERT: X 182 ASP cc_start: 0.8171 (t70) cc_final: 0.7579 (t0) REVERT: X 196 ILE cc_start: 0.8103 (mt) cc_final: 0.7862 (mp) REVERT: X 221 GLU cc_start: 0.7774 (tp30) cc_final: 0.7307 (tt0) REVERT: X 229 TYR cc_start: 0.7499 (m-80) cc_final: 0.7011 (m-80) REVERT: X 232 LEU cc_start: 0.8747 (tp) cc_final: 0.8428 (mm) REVERT: X 242 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7463 (mp0) REVERT: X 243 ILE cc_start: 0.7755 (mt) cc_final: 0.7471 (mp) REVERT: X 264 ASP cc_start: 0.7315 (p0) cc_final: 0.7036 (p0) REVERT: X 271 GLN cc_start: 0.7837 (mt0) cc_final: 0.7491 (mm-40) REVERT: X 282 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6801 (tm-30) REVERT: X 317 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6795 (m-30) REVERT: X 341 ASN cc_start: 0.8520 (p0) cc_final: 0.8212 (p0) REVERT: X 351 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6974 (mm-30) REVERT: Y 26 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8193 (mp) REVERT: Y 69 ARG cc_start: 0.8072 (mtt90) cc_final: 0.7770 (mmm-85) REVERT: Y 106 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7971 (mp) REVERT: Y 129 ILE cc_start: 0.8203 (mm) cc_final: 0.7996 (mm) REVERT: Y 130 LYS cc_start: 0.8168 (ttmm) cc_final: 0.7921 (ttpp) REVERT: Y 176 ILE cc_start: 0.6405 (mm) cc_final: 0.6120 (mp) REVERT: Y 236 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8158 (t) REVERT: Y 272 GLN cc_start: 0.7214 (tt0) cc_final: 0.6995 (tt0) REVERT: Y 282 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7410 (tp30) REVERT: Y 297 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7719 (mm-30) REVERT: Y 317 PHE cc_start: 0.8481 (m-80) cc_final: 0.8078 (m-80) REVERT: Y 350 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7096 (mtp85) REVERT: Y 357 LYS cc_start: 0.8409 (mttm) cc_final: 0.7937 (mmmm) REVERT: Y 378 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7198 (mt-10) REVERT: Q 1021 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: Q 1030 THR cc_start: 0.7988 (p) cc_final: 0.7367 (p) REVERT: Q 1078 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7222 (mtm-85) REVERT: Q 1087 ARG cc_start: 0.7764 (mtm110) cc_final: 0.7534 (mtm-85) REVERT: Q 1092 ASP cc_start: 0.7531 (m-30) cc_final: 0.7197 (m-30) REVERT: Q 1103 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.6356 (p0) REVERT: Q 1112 LYS cc_start: 0.8256 (mtpp) cc_final: 0.8015 (mtmm) REVERT: Q 1123 GLU cc_start: 0.7655 (mp0) cc_final: 0.7320 (mp0) REVERT: Q 1134 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7515 (mm-30) REVERT: Q 1160 LYS cc_start: 0.7816 (ptpp) cc_final: 0.7553 (ptpp) REVERT: Q 1167 PHE cc_start: 0.7949 (p90) cc_final: 0.7729 (p90) REVERT: Q 1176 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6926 (mm-30) REVERT: Q 1200 ARG cc_start: 0.7627 (mtm110) cc_final: 0.7249 (mtp85) REVERT: Q 1231 ASN cc_start: 0.7827 (m-40) cc_final: 0.7559 (m-40) REVERT: Q 1239 ASP cc_start: 0.7120 (t0) cc_final: 0.6770 (t70) REVERT: Q 1242 ILE cc_start: 0.7739 (mm) cc_final: 0.7439 (mt) REVERT: Q 1260 LYS cc_start: 0.8318 (mtpp) cc_final: 0.8062 (mtpp) REVERT: Q 1266 GLU cc_start: 0.7691 (mp0) cc_final: 0.7143 (mp0) REVERT: Q 1280 LYS cc_start: 0.8016 (ptpp) cc_final: 0.7687 (ptpp) REVERT: Q 1316 HIS cc_start: 0.8159 (m-70) cc_final: 0.7484 (m-70) REVERT: Q 1371 LEU cc_start: 0.7410 (mp) cc_final: 0.7100 (pt) REVERT: Q 1405 MET cc_start: 0.6849 (tmm) cc_final: 0.6508 (mmm) outliers start: 126 outliers final: 73 residues processed: 883 average time/residue: 1.5968 time to fit residues: 1612.5990 Evaluate side-chains 921 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 828 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 132 ASN Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 146 GLN Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 591 LEU Chi-restraints excluded: chain R residue 648 LYS Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 147 MET Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 253 ASP Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain T residue 398 SER Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 239 VAL Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 281 LYS Chi-restraints excluded: chain U residue 346 ASP Chi-restraints excluded: chain U residue 350 ARG Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 389 THR Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 398 SER Chi-restraints excluded: chain V residue 443 LYS Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 373 GLN Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 241 LYS Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 454 LYS Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 238 THR Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 346 ASP Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 361 GLU Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 440 VAL Chi-restraints excluded: chain Q residue 950 ILE Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1091 GLU Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1103 ASP Chi-restraints excluded: chain Q residue 1193 VAL Chi-restraints excluded: chain Q residue 1288 MET Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1343 ILE Chi-restraints excluded: chain Q residue 1389 VAL Chi-restraints excluded: chain Z residue 315 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 610 HIS R 633 GLN ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 310 ASN V 51 GLN V 263 GLN ** V 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 173 ASN W 230 GLN W 360 ASN X 289 ASN X 325 ASN Y 373 GLN Q1244 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.093 29102 Z= 0.676 Angle : 0.772 12.899 39373 Z= 0.387 Chirality : 0.054 0.264 4620 Planarity : 0.005 0.059 5040 Dihedral : 7.258 129.817 4004 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.25 % Allowed : 28.00 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3618 helix: 0.30 (0.13), residues: 1508 sheet: 0.37 (0.19), residues: 664 loop : -1.12 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP Y 280 HIS 0.010 0.002 HIS R 191 PHE 0.026 0.003 PHE R 691 TYR 0.038 0.003 TYR V 462 ARG 0.012 0.001 ARG S 73 *********************** 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 1002 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 836 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.7851 (p0) cc_final: 0.7273 (p0) REVERT: R 38 SER cc_start: 0.8031 (t) cc_final: 0.7670 (m) REVERT: R 69 LYS cc_start: 0.7925 (mtpt) cc_final: 0.7678 (mtpt) REVERT: R 70 PHE cc_start: 0.6808 (t80) cc_final: 0.6512 (t80) REVERT: R 113 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: R 193 ASP cc_start: 0.7348 (p0) cc_final: 0.7018 (p0) REVERT: R 242 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6130 (mp10) REVERT: R 249 ASP cc_start: 0.7713 (m-30) cc_final: 0.7196 (m-30) REVERT: R 258 ASP cc_start: 0.7638 (m-30) cc_final: 0.7399 (m-30) REVERT: R 609 GLN cc_start: 0.7929 (mt0) cc_final: 0.7587 (mt0) REVERT: R 617 GLU cc_start: 0.8152 (mp0) cc_final: 0.7940 (mp0) REVERT: R 623 GLU cc_start: 0.8156 (tp30) cc_final: 0.7322 (tm-30) REVERT: R 705 ASP cc_start: 0.7295 (t0) cc_final: 0.6993 (t0) REVERT: R 719 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6795 (mpp80) REVERT: R 733 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6874 (mt-10) REVERT: R 743 LYS cc_start: 0.7708 (tptm) cc_final: 0.7090 (ttmp) REVERT: S 159 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7479 (ptm160) REVERT: T 31 LYS cc_start: 0.8419 (mmtp) cc_final: 0.8186 (mmtm) REVERT: T 76 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7988 (tp) REVERT: T 141 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: T 205 ASN cc_start: 0.7543 (m-40) cc_final: 0.7108 (m-40) REVERT: T 216 ASP cc_start: 0.8276 (t70) cc_final: 0.7868 (m-30) REVERT: T 282 GLU cc_start: 0.7111 (pm20) cc_final: 0.6765 (pm20) REVERT: T 312 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7853 (mp0) REVERT: T 330 SER cc_start: 0.8368 (m) cc_final: 0.7653 (p) REVERT: T 386 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7431 (mpt180) REVERT: T 392 ARG cc_start: 0.7557 (mtm110) cc_final: 0.7269 (mtm180) REVERT: T 393 LEU cc_start: 0.7787 (mt) cc_final: 0.7586 (mt) REVERT: T 436 VAL cc_start: 0.7563 (t) cc_final: 0.7351 (t) REVERT: U 32 ASP cc_start: 0.7651 (m-30) cc_final: 0.7403 (m-30) REVERT: U 71 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7964 (t) REVERT: U 110 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6765 (pp20) REVERT: U 127 ILE cc_start: 0.8550 (mt) cc_final: 0.8338 (mp) REVERT: U 134 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7222 (tp30) REVERT: U 142 GLU cc_start: 0.7530 (tt0) cc_final: 0.7105 (tm-30) REVERT: U 143 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7580 (mt) REVERT: U 155 GLN cc_start: 0.7193 (mt0) cc_final: 0.6970 (mt0) REVERT: U 174 LYS cc_start: 0.7477 (mtpt) cc_final: 0.7244 (mtpt) REVERT: U 193 ASP cc_start: 0.8129 (t0) cc_final: 0.7631 (t0) REVERT: U 255 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7580 (mp) REVERT: U 271 ASP cc_start: 0.7094 (m-30) cc_final: 0.6873 (m-30) REVERT: U 282 GLU cc_start: 0.7834 (tp30) cc_final: 0.7505 (tp30) REVERT: U 300 MET cc_start: 0.8657 (mmm) cc_final: 0.8350 (mmm) REVERT: U 362 GLN cc_start: 0.6854 (tp40) cc_final: 0.6558 (mm-40) REVERT: U 393 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: U 403 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7584 (mt) REVERT: U 451 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7660 (mp10) REVERT: V 36 ASP cc_start: 0.7513 (m-30) cc_final: 0.7219 (p0) REVERT: V 42 LYS cc_start: 0.7845 (mtmm) cc_final: 0.6974 (tttm) REVERT: V 109 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7175 (mm-30) REVERT: V 111 TYR cc_start: 0.8307 (m-80) cc_final: 0.8061 (m-80) REVERT: V 135 GLU cc_start: 0.7830 (tt0) cc_final: 0.7421 (tt0) REVERT: V 148 THR cc_start: 0.8069 (m) cc_final: 0.7516 (p) REVERT: V 154 ASN cc_start: 0.7661 (t0) cc_final: 0.7313 (t0) REVERT: V 203 GLU cc_start: 0.8141 (tt0) cc_final: 0.7782 (tt0) REVERT: V 214 ARG cc_start: 0.7570 (mmt180) cc_final: 0.7120 (mmp-170) REVERT: V 216 ASP cc_start: 0.7210 (p0) cc_final: 0.6962 (p0) REVERT: V 221 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6863 (tm-30) REVERT: V 234 LYS cc_start: 0.7658 (mtpt) cc_final: 0.7437 (mtpt) REVERT: V 236 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7662 (mm-30) REVERT: V 317 ASP cc_start: 0.7969 (m-30) cc_final: 0.7469 (m-30) REVERT: V 329 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7461 (tm-30) REVERT: V 354 ILE cc_start: 0.7827 (mt) cc_final: 0.7547 (mm) REVERT: V 389 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.7359 (p) REVERT: W 36 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7303 (mm-40) REVERT: W 130 LYS cc_start: 0.7950 (ttmm) cc_final: 0.7704 (ttpp) REVERT: W 181 LYS cc_start: 0.7589 (ttpp) cc_final: 0.7292 (ttmt) REVERT: W 182 GLU cc_start: 0.7466 (tp30) cc_final: 0.6852 (tm-30) REVERT: W 184 VAL cc_start: 0.8297 (m) cc_final: 0.7732 (t) REVERT: W 198 LYS cc_start: 0.8334 (tttt) cc_final: 0.8051 (tttt) REVERT: W 208 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6710 (ttt-90) REVERT: W 220 ARG cc_start: 0.7234 (mpp80) cc_final: 0.6948 (mpp80) REVERT: W 226 GLU cc_start: 0.7196 (mp0) cc_final: 0.6660 (mp0) REVERT: W 283 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6649 (tm-30) REVERT: W 285 LYS cc_start: 0.8143 (ttmm) cc_final: 0.7807 (ttpp) REVERT: W 333 ARG cc_start: 0.8288 (mtm180) cc_final: 0.8064 (mtp180) REVERT: W 338 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8265 (mttm) REVERT: W 374 GLU cc_start: 0.7133 (tp30) cc_final: 0.6637 (tp30) REVERT: W 378 GLU cc_start: 0.7768 (mp0) cc_final: 0.7394 (mm-30) REVERT: W 385 ASP cc_start: 0.7213 (m-30) cc_final: 0.6795 (m-30) REVERT: W 389 LYS cc_start: 0.7592 (mmmm) cc_final: 0.7207 (mmmm) REVERT: W 393 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6652 (mt-10) REVERT: W 413 ARG cc_start: 0.7979 (mtm180) cc_final: 0.7467 (ptp90) REVERT: W 419 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6501 (mp0) REVERT: W 421 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: W 425 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7462 (ttt90) REVERT: X 37 GLU cc_start: 0.7727 (pp20) cc_final: 0.7384 (pp20) REVERT: X 45 GLU cc_start: 0.7130 (tp30) cc_final: 0.6383 (tt0) REVERT: X 94 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6774 (mp10) REVERT: X 95 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7314 (mm-30) REVERT: X 134 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7725 (ptpp) REVERT: X 135 GLU cc_start: 0.7187 (tt0) cc_final: 0.6623 (mt-10) REVERT: X 150 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7187 (tt0) REVERT: X 156 LEU cc_start: 0.8731 (mt) cc_final: 0.8513 (OUTLIER) REVERT: X 177 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7892 (ttmm) REVERT: X 182 ASP cc_start: 0.8231 (t70) cc_final: 0.7745 (t0) REVERT: X 192 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7383 (mm-30) REVERT: X 196 ILE cc_start: 0.8043 (mt) cc_final: 0.7796 (mp) REVERT: X 221 GLU cc_start: 0.7802 (tp30) cc_final: 0.7414 (tp30) REVERT: X 223 ASP cc_start: 0.7831 (m-30) cc_final: 0.7566 (m-30) REVERT: X 229 TYR cc_start: 0.7517 (m-80) cc_final: 0.7002 (m-80) REVERT: X 230 VAL cc_start: 0.8201 (t) cc_final: 0.7762 (p) REVERT: X 232 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8574 (mm) REVERT: X 242 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7406 (mp0) REVERT: X 243 ILE cc_start: 0.7726 (mt) cc_final: 0.7435 (mp) REVERT: X 264 ASP cc_start: 0.7175 (p0) cc_final: 0.6935 (p0) REVERT: X 282 GLU cc_start: 0.7498 (tm-30) cc_final: 0.6929 (tm-30) REVERT: X 317 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6972 (m-30) REVERT: X 341 ASN cc_start: 0.8479 (p0) cc_final: 0.8225 (p0) REVERT: X 351 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6974 (mm-30) REVERT: Y 69 ARG cc_start: 0.8139 (mtt90) cc_final: 0.7729 (mmt-90) REVERT: Y 81 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7020 (mtmm) REVERT: Y 106 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7943 (mp) REVERT: Y 130 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7965 (ttpp) REVERT: Y 202 LEU cc_start: 0.8240 (mp) cc_final: 0.8002 (mt) REVERT: Y 236 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8129 (t) REVERT: Y 282 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7451 (mm-30) REVERT: Y 297 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7786 (mm-30) REVERT: Y 350 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7254 (mtp85) REVERT: Y 357 LYS cc_start: 0.8462 (mttm) cc_final: 0.8135 (mtpp) REVERT: Y 378 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7250 (mt-10) REVERT: Y 404 SER cc_start: 0.8183 (t) cc_final: 0.7549 (m) REVERT: Q 1021 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7657 (m-30) REVERT: Q 1087 ARG cc_start: 0.7737 (mtm110) cc_final: 0.6798 (mtm-85) REVERT: Q 1091 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: Q 1092 ASP cc_start: 0.7511 (m-30) cc_final: 0.7158 (m-30) REVERT: Q 1103 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7040 (p0) REVERT: Q 1123 GLU cc_start: 0.7658 (mp0) cc_final: 0.7300 (mp0) REVERT: Q 1134 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7549 (mm-30) REVERT: Q 1160 LYS cc_start: 0.7854 (ptpp) cc_final: 0.7529 (ptpp) REVERT: Q 1176 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6812 (mm-30) REVERT: Q 1189 SER cc_start: 0.7869 (t) cc_final: 0.7403 (p) REVERT: Q 1200 ARG cc_start: 0.7718 (mtm110) cc_final: 0.7247 (mtp85) REVERT: Q 1231 ASN cc_start: 0.7825 (m-40) cc_final: 0.7562 (m-40) REVERT: Q 1239 ASP cc_start: 0.7169 (t0) cc_final: 0.6873 (t70) REVERT: Q 1242 ILE cc_start: 0.7686 (mm) cc_final: 0.7439 (mt) REVERT: Q 1260 LYS cc_start: 0.8332 (mtpp) cc_final: 0.8068 (mtpp) REVERT: Q 1266 GLU cc_start: 0.7694 (mp0) cc_final: 0.7160 (mp0) REVERT: Q 1280 LYS cc_start: 0.8023 (ptpp) cc_final: 0.7706 (ptpp) REVERT: Q 1316 HIS cc_start: 0.8046 (m-70) cc_final: 0.7389 (m-70) REVERT: Q 1371 LEU cc_start: 0.7364 (mp) cc_final: 0.7098 (pt) REVERT: Q 1405 MET cc_start: 0.6903 (tmm) cc_final: 0.6542 (mmm) REVERT: Q 1431 ARG cc_start: 0.6564 (OUTLIER) cc_final: 0.6060 (tmm160) outliers start: 166 outliers final: 89 residues processed: 921 average time/residue: 1.6589 time to fit residues: 1742.0897 Evaluate side-chains 928 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 811 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 132 ASN Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 591 LEU Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 147 MET Chi-restraints excluded: chain S residue 159 ARG Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 253 ASP Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 345 THR Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 239 VAL Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 281 LYS Chi-restraints excluded: chain U residue 331 LYS Chi-restraints excluded: chain U residue 350 ARG Chi-restraints excluded: chain U residue 393 GLU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 322 THR Chi-restraints excluded: chain V residue 353 VAL Chi-restraints excluded: chain V residue 389 THR Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 398 SER Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain V residue 462 TYR Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 233 LYS Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 338 LYS Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 373 GLN Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 138 GLU Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 232 LEU Chi-restraints excluded: chain X residue 241 LYS Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 377 LYS Chi-restraints excluded: chain X residue 454 LYS Chi-restraints excluded: chain Y residue 81 LYS Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 180 THR Chi-restraints excluded: chain Y residue 188 ASP Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 238 THR Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 361 GLU Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 440 VAL Chi-restraints excluded: chain Q residue 950 ILE Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1035 THR Chi-restraints excluded: chain Q residue 1091 GLU Chi-restraints excluded: chain Q residue 1103 ASP Chi-restraints excluded: chain Q residue 1193 VAL Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1324 MET Chi-restraints excluded: chain Q residue 1343 ILE Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain Q residue 1389 VAL Chi-restraints excluded: chain Q residue 1431 ARG Chi-restraints excluded: chain Z residue 315 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 0.9990 chunk 333 optimal weight: 0.5980 chunk 304 optimal weight: 0.8980 chunk 324 optimal weight: 0.7980 chunk 195 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 chunk 254 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 292 optimal weight: 0.9980 chunk 306 optimal weight: 0.6980 chunk 323 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN U 360 ASN V 51 GLN V 263 GLN ** V 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 394 GLN V 417 GLN ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 173 ASN W 360 ASN X 124 ASN X 271 GLN X 289 ASN X 325 ASN X 430 ASN Y 49 GLN Y 310 ASN Q1244 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29102 Z= 0.243 Angle : 0.611 10.584 39373 Z= 0.300 Chirality : 0.044 0.248 4620 Planarity : 0.004 0.040 5040 Dihedral : 6.790 123.429 4004 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.45 % Allowed : 30.62 % Favored : 65.93 % 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: -0.07 (0.14), residues: 3618 helix: 0.72 (0.14), residues: 1504 sheet: 0.38 (0.20), residues: 651 loop : -1.00 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 280 HIS 0.010 0.001 HIS Y 25 PHE 0.021 0.001 PHE R 691 TYR 0.033 0.002 TYR R 724 ARG 0.012 0.000 ARG S 73 *********************** 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 925 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 816 time to evaluate : 3.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.7839 (p0) cc_final: 0.7233 (p0) REVERT: R 38 SER cc_start: 0.7989 (t) cc_final: 0.7610 (m) REVERT: R 69 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7652 (mtpt) REVERT: R 70 PHE cc_start: 0.6820 (t80) cc_final: 0.6501 (t80) REVERT: R 75 LEU cc_start: 0.8630 (mm) cc_final: 0.8306 (tm) REVERT: R 113 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: R 193 ASP cc_start: 0.7282 (p0) cc_final: 0.6949 (p0) REVERT: R 237 LYS cc_start: 0.7714 (mmpt) cc_final: 0.7495 (mmpt) REVERT: R 258 ASP cc_start: 0.7728 (m-30) cc_final: 0.7480 (m-30) REVERT: R 609 GLN cc_start: 0.7946 (mt0) cc_final: 0.7591 (mt0) REVERT: R 617 GLU cc_start: 0.8138 (mp0) cc_final: 0.7928 (mp0) REVERT: R 623 GLU cc_start: 0.8121 (tp30) cc_final: 0.7318 (tm-30) REVERT: R 676 LYS cc_start: 0.4385 (pttm) cc_final: 0.3488 (pttp) REVERT: R 705 ASP cc_start: 0.7337 (t0) cc_final: 0.7085 (t0) REVERT: R 719 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6802 (mpp80) REVERT: R 735 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: R 743 LYS cc_start: 0.7713 (tptm) cc_final: 0.7277 (mttp) REVERT: S 141 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6944 (mm-40) REVERT: T 31 LYS cc_start: 0.8402 (mmtp) cc_final: 0.8103 (mmtt) REVERT: T 76 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7865 (tp) REVERT: T 141 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7567 (tp30) REVERT: T 205 ASN cc_start: 0.7494 (m-40) cc_final: 0.7098 (m-40) REVERT: T 216 ASP cc_start: 0.8212 (t70) cc_final: 0.7784 (m-30) REVERT: T 282 GLU cc_start: 0.7168 (pm20) cc_final: 0.6834 (pm20) REVERT: T 312 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7844 (mp0) REVERT: T 330 SER cc_start: 0.8280 (m) cc_final: 0.7766 (t) REVERT: T 332 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7273 (tp) REVERT: T 386 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7464 (mpt180) REVERT: T 392 ARG cc_start: 0.7592 (mtm110) cc_final: 0.7078 (mtm-85) REVERT: T 393 LEU cc_start: 0.7711 (mt) cc_final: 0.7484 (mt) REVERT: T 436 VAL cc_start: 0.7553 (t) cc_final: 0.7332 (t) REVERT: U 32 ASP cc_start: 0.7684 (m-30) cc_final: 0.7367 (m-30) REVERT: U 110 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6815 (pp20) REVERT: U 127 ILE cc_start: 0.8538 (mt) cc_final: 0.8328 (mp) REVERT: U 134 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7272 (tp30) REVERT: U 142 GLU cc_start: 0.7461 (tt0) cc_final: 0.7064 (tm-30) REVERT: U 143 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7516 (mt) REVERT: U 155 GLN cc_start: 0.7116 (mt0) cc_final: 0.6897 (mt0) REVERT: U 174 LYS cc_start: 0.7440 (mtpt) cc_final: 0.7181 (mtpt) REVERT: U 255 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7546 (mp) REVERT: U 271 ASP cc_start: 0.7140 (m-30) cc_final: 0.6751 (m-30) REVERT: U 282 GLU cc_start: 0.7775 (tp30) cc_final: 0.7405 (tp30) REVERT: U 297 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8053 (mp0) REVERT: U 300 MET cc_start: 0.8636 (mmm) cc_final: 0.8269 (mmm) REVERT: U 362 GLN cc_start: 0.6823 (tp40) cc_final: 0.6522 (mm-40) REVERT: U 451 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7663 (mp10) REVERT: V 36 ASP cc_start: 0.7530 (m-30) cc_final: 0.7233 (p0) REVERT: V 42 LYS cc_start: 0.7736 (mtmm) cc_final: 0.6939 (tttm) REVERT: V 109 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7230 (mm-30) REVERT: V 111 TYR cc_start: 0.8268 (m-80) cc_final: 0.7979 (m-80) REVERT: V 135 GLU cc_start: 0.7827 (tt0) cc_final: 0.7406 (tt0) REVERT: V 148 THR cc_start: 0.8091 (m) cc_final: 0.7550 (p) REVERT: V 154 ASN cc_start: 0.7641 (t0) cc_final: 0.7292 (t0) REVERT: V 168 VAL cc_start: 0.8107 (p) cc_final: 0.7868 (t) REVERT: V 203 GLU cc_start: 0.8112 (tt0) cc_final: 0.7778 (tt0) REVERT: V 214 ARG cc_start: 0.7465 (mmt180) cc_final: 0.7103 (mmp-170) REVERT: V 216 ASP cc_start: 0.7195 (p0) cc_final: 0.6939 (p0) REVERT: V 221 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6874 (tm-30) REVERT: V 236 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7567 (mm-30) REVERT: V 287 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7558 (mm-30) REVERT: V 311 ASP cc_start: 0.7919 (t0) cc_final: 0.7487 (t70) REVERT: V 317 ASP cc_start: 0.7864 (m-30) cc_final: 0.7327 (m-30) REVERT: V 329 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7544 (tm-30) REVERT: V 354 ILE cc_start: 0.7837 (mt) cc_final: 0.7554 (mm) REVERT: V 385 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7289 (mm-30) REVERT: V 394 GLN cc_start: 0.7423 (pt0) cc_final: 0.6970 (pt0) REVERT: W 36 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7216 (mm110) REVERT: W 130 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7705 (ttpp) REVERT: W 181 LYS cc_start: 0.7649 (ttpp) cc_final: 0.7347 (ttmt) REVERT: W 182 GLU cc_start: 0.7475 (tp30) cc_final: 0.6928 (tm-30) REVERT: W 198 LYS cc_start: 0.8358 (tttt) cc_final: 0.8085 (tttt) REVERT: W 208 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6669 (ttt-90) REVERT: W 220 ARG cc_start: 0.7219 (mpp80) cc_final: 0.6942 (mpp80) REVERT: W 283 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6794 (tm-30) REVERT: W 285 LYS cc_start: 0.8097 (ttmm) cc_final: 0.7758 (ttpp) REVERT: W 338 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8247 (mttp) REVERT: W 374 GLU cc_start: 0.7007 (tp30) cc_final: 0.6541 (tp30) REVERT: W 385 ASP cc_start: 0.7193 (m-30) cc_final: 0.6741 (m-30) REVERT: W 389 LYS cc_start: 0.7570 (mmmm) cc_final: 0.7179 (mmmm) REVERT: W 393 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6394 (mt-10) REVERT: W 413 ARG cc_start: 0.7812 (mtm180) cc_final: 0.7274 (ptp90) REVERT: W 419 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6548 (mp0) REVERT: W 421 GLU cc_start: 0.7800 (pm20) cc_final: 0.7581 (mp0) REVERT: W 425 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7376 (ttt90) REVERT: X 37 GLU cc_start: 0.7720 (pp20) cc_final: 0.7372 (pp20) REVERT: X 45 GLU cc_start: 0.7166 (tp30) cc_final: 0.6397 (tt0) REVERT: X 94 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6584 (mp10) REVERT: X 125 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7506 (t80) REVERT: X 134 LYS cc_start: 0.8116 (ptpt) cc_final: 0.7709 (ptpp) REVERT: X 135 GLU cc_start: 0.7193 (tt0) cc_final: 0.6602 (mt-10) REVERT: X 143 GLU cc_start: 0.7675 (tt0) cc_final: 0.7185 (tt0) REVERT: X 150 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7154 (tt0) REVERT: X 156 LEU cc_start: 0.8692 (mt) cc_final: 0.8467 (OUTLIER) REVERT: X 177 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7875 (ttmm) REVERT: X 182 ASP cc_start: 0.8241 (t70) cc_final: 0.7670 (t0) REVERT: X 196 ILE cc_start: 0.8079 (mt) cc_final: 0.7847 (mp) REVERT: X 221 GLU cc_start: 0.7800 (tp30) cc_final: 0.7400 (tp30) REVERT: X 229 TYR cc_start: 0.7480 (m-80) cc_final: 0.7022 (m-80) REVERT: X 230 VAL cc_start: 0.8169 (t) cc_final: 0.7750 (p) REVERT: X 232 LEU cc_start: 0.8717 (tp) cc_final: 0.8493 (mm) REVERT: X 242 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7375 (mp0) REVERT: X 243 ILE cc_start: 0.7736 (mt) cc_final: 0.7448 (mp) REVERT: X 264 ASP cc_start: 0.7215 (p0) cc_final: 0.6970 (p0) REVERT: X 282 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6842 (tm-30) REVERT: X 317 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6819 (m-30) REVERT: X 341 ASN cc_start: 0.8485 (p0) cc_final: 0.8241 (p0) REVERT: X 351 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6946 (mm-30) REVERT: X 396 GLU cc_start: 0.6664 (tm-30) cc_final: 0.6140 (tm-30) REVERT: Y 69 ARG cc_start: 0.8128 (mtt90) cc_final: 0.7852 (mmm-85) REVERT: Y 106 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7969 (mp) REVERT: Y 130 LYS cc_start: 0.8163 (ttmm) cc_final: 0.7933 (ttpp) REVERT: Y 236 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8130 (t) REVERT: Y 272 GLN cc_start: 0.7238 (tt0) cc_final: 0.6954 (tt0) REVERT: Y 282 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7430 (tp30) REVERT: Y 297 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7731 (mm-30) REVERT: Y 350 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7226 (mtp85) REVERT: Y 357 LYS cc_start: 0.8397 (mttm) cc_final: 0.8072 (mtpp) REVERT: Y 378 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7268 (mt-10) REVERT: Q 1021 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7665 (m-30) REVERT: Q 1030 THR cc_start: 0.7899 (p) cc_final: 0.7280 (p) REVERT: Q 1078 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7384 (mtm-85) REVERT: Q 1087 ARG cc_start: 0.7774 (mtm110) cc_final: 0.7546 (mtm-85) REVERT: Q 1092 ASP cc_start: 0.7486 (m-30) cc_final: 0.7091 (m-30) REVERT: Q 1123 GLU cc_start: 0.7650 (mp0) cc_final: 0.7301 (mp0) REVERT: Q 1134 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7501 (mm-30) REVERT: Q 1160 LYS cc_start: 0.7859 (ptpp) cc_final: 0.7562 (ptpp) REVERT: Q 1176 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6849 (mm-30) REVERT: Q 1189 SER cc_start: 0.7926 (t) cc_final: 0.7514 (p) REVERT: Q 1200 ARG cc_start: 0.7676 (mtm110) cc_final: 0.7268 (mtp85) REVERT: Q 1231 ASN cc_start: 0.7826 (m-40) cc_final: 0.7538 (m-40) REVERT: Q 1239 ASP cc_start: 0.7129 (t0) cc_final: 0.6818 (t70) REVERT: Q 1242 ILE cc_start: 0.7745 (mm) cc_final: 0.7525 (mt) REVERT: Q 1260 LYS cc_start: 0.8311 (mtpp) cc_final: 0.8054 (mtpp) REVERT: Q 1266 GLU cc_start: 0.7692 (mp0) cc_final: 0.7129 (mp0) REVERT: Q 1280 LYS cc_start: 0.7988 (ptpp) cc_final: 0.7656 (ptpp) REVERT: Q 1316 HIS cc_start: 0.8098 (m-70) cc_final: 0.7424 (m-70) REVERT: Q 1327 MET cc_start: 0.5118 (pmm) cc_final: 0.4467 (pmm) REVERT: Q 1371 LEU cc_start: 0.7331 (mp) cc_final: 0.7095 (pt) REVERT: Q 1405 MET cc_start: 0.6840 (tmm) cc_final: 0.6497 (mmm) REVERT: Q 1432 MET cc_start: 0.3946 (mpp) cc_final: 0.3487 (mpp) outliers start: 109 outliers final: 60 residues processed: 870 average time/residue: 1.6623 time to fit residues: 1647.1625 Evaluate side-chains 887 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 808 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 132 ASN Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 591 LEU Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 147 MET Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 253 ASP Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 239 VAL Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 398 SER Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 233 LYS Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 338 LYS Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 373 GLN Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 138 GLU Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 241 LYS Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 238 THR Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 361 GLU Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 440 VAL Chi-restraints excluded: chain Q residue 950 ILE Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1091 GLU Chi-restraints excluded: chain Q residue 1103 ASP Chi-restraints excluded: chain Q residue 1193 VAL Chi-restraints excluded: chain Q residue 1288 MET Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1389 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 0.5980 chunk 342 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 359 optimal weight: 0.6980 chunk 331 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 175 optimal weight: 0.1980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 633 GLN ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 GLN V 263 GLN V 417 GLN ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 173 ASN W 360 ASN X 289 ASN X 325 ASN X 430 ASN Y 49 GLN Y 310 ASN Q1244 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29102 Z= 0.290 Angle : 0.623 11.039 39373 Z= 0.305 Chirality : 0.044 0.256 4620 Planarity : 0.004 0.039 5040 Dihedral : 6.722 125.733 4004 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.10 % Allowed : 31.10 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3618 helix: 0.80 (0.14), residues: 1507 sheet: 0.38 (0.20), residues: 652 loop : -0.98 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Y 280 HIS 0.005 0.001 HIS Y 25 PHE 0.019 0.001 PHE R 691 TYR 0.019 0.002 TYR V 462 ARG 0.013 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 920 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 822 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.7840 (p0) cc_final: 0.7230 (p0) REVERT: R 38 SER cc_start: 0.7956 (t) cc_final: 0.7579 (m) REVERT: R 69 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7673 (mtpt) REVERT: R 70 PHE cc_start: 0.6786 (t80) cc_final: 0.6464 (t80) REVERT: R 75 LEU cc_start: 0.8616 (mm) cc_final: 0.8271 (tm) REVERT: R 101 ASP cc_start: 0.7510 (t70) cc_final: 0.7184 (t70) REVERT: R 113 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: R 121 HIS cc_start: 0.8414 (m-70) cc_final: 0.8060 (m-70) REVERT: R 146 GLN cc_start: 0.7710 (mm110) cc_final: 0.7375 (mm-40) REVERT: R 193 ASP cc_start: 0.7270 (p0) cc_final: 0.6912 (p0) REVERT: R 237 LYS cc_start: 0.7715 (mmpt) cc_final: 0.7499 (mmpt) REVERT: R 258 ASP cc_start: 0.7724 (m-30) cc_final: 0.7480 (m-30) REVERT: R 268 GLU cc_start: 0.8143 (pm20) cc_final: 0.7821 (pm20) REVERT: R 609 GLN cc_start: 0.7936 (mt0) cc_final: 0.7596 (mt0) REVERT: R 623 GLU cc_start: 0.8125 (tp30) cc_final: 0.7335 (tm-30) REVERT: R 643 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7283 (tp30) REVERT: R 705 ASP cc_start: 0.7338 (t0) cc_final: 0.7077 (t0) REVERT: R 719 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6769 (mpp80) REVERT: R 733 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6820 (mt-10) REVERT: R 735 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7282 (mm-30) REVERT: R 743 LYS cc_start: 0.7717 (tptm) cc_final: 0.6985 (ttmp) REVERT: S 141 GLN cc_start: 0.7198 (mm-40) cc_final: 0.6870 (mm-40) REVERT: T 31 LYS cc_start: 0.8394 (mmtp) cc_final: 0.8096 (mmtt) REVERT: T 76 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7879 (tp) REVERT: T 109 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7551 (mt-10) REVERT: T 141 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: T 205 ASN cc_start: 0.7547 (m-40) cc_final: 0.7148 (m-40) REVERT: T 216 ASP cc_start: 0.8199 (t70) cc_final: 0.7770 (m-30) REVERT: T 282 GLU cc_start: 0.7115 (pm20) cc_final: 0.6785 (pm20) REVERT: T 312 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7854 (mp0) REVERT: T 330 SER cc_start: 0.8258 (m) cc_final: 0.7752 (t) REVERT: T 332 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7279 (tp) REVERT: T 386 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7470 (mpt180) REVERT: T 392 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7077 (mtm-85) REVERT: T 393 LEU cc_start: 0.7694 (mt) cc_final: 0.7466 (mt) REVERT: T 436 VAL cc_start: 0.7527 (t) cc_final: 0.7308 (t) REVERT: U 32 ASP cc_start: 0.7683 (m-30) cc_final: 0.7357 (m-30) REVERT: U 110 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6812 (pp20) REVERT: U 127 ILE cc_start: 0.8546 (mt) cc_final: 0.8329 (mp) REVERT: U 134 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7289 (tp30) REVERT: U 142 GLU cc_start: 0.7478 (tt0) cc_final: 0.7090 (tm-30) REVERT: U 143 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7498 (mt) REVERT: U 155 GLN cc_start: 0.7125 (mt0) cc_final: 0.6913 (mt0) REVERT: U 174 LYS cc_start: 0.7442 (mtpt) cc_final: 0.7181 (mtpt) REVERT: U 201 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7503 (mtmt) REVERT: U 255 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7545 (mp) REVERT: U 271 ASP cc_start: 0.7138 (m-30) cc_final: 0.6738 (m-30) REVERT: U 282 GLU cc_start: 0.7776 (tp30) cc_final: 0.7409 (tp30) REVERT: U 297 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8043 (mp0) REVERT: U 300 MET cc_start: 0.8647 (mmm) cc_final: 0.8287 (mmm) REVERT: U 362 GLN cc_start: 0.6824 (tp40) cc_final: 0.6516 (mm-40) REVERT: U 451 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7663 (mp10) REVERT: V 36 ASP cc_start: 0.7524 (m-30) cc_final: 0.7295 (p0) REVERT: V 42 LYS cc_start: 0.7741 (mtmm) cc_final: 0.6863 (tttm) REVERT: V 68 LYS cc_start: 0.7977 (mttp) cc_final: 0.7720 (mtpp) REVERT: V 109 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7232 (mm-30) REVERT: V 111 TYR cc_start: 0.8255 (m-80) cc_final: 0.7958 (m-80) REVERT: V 135 GLU cc_start: 0.7817 (tt0) cc_final: 0.7401 (tt0) REVERT: V 144 VAL cc_start: 0.8171 (t) cc_final: 0.7863 (m) REVERT: V 146 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7241 (pp20) REVERT: V 148 THR cc_start: 0.8099 (m) cc_final: 0.7576 (p) REVERT: V 154 ASN cc_start: 0.7640 (t0) cc_final: 0.7296 (t0) REVERT: V 168 VAL cc_start: 0.8081 (p) cc_final: 0.7780 (t) REVERT: V 203 GLU cc_start: 0.8105 (tt0) cc_final: 0.7795 (tt0) REVERT: V 214 ARG cc_start: 0.7461 (mmt180) cc_final: 0.7094 (mmp-170) REVERT: V 216 ASP cc_start: 0.7191 (p0) cc_final: 0.6919 (p0) REVERT: V 221 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6892 (tm-30) REVERT: V 236 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7571 (mm-30) REVERT: V 287 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7587 (mm-30) REVERT: V 311 ASP cc_start: 0.7897 (t0) cc_final: 0.7550 (t0) REVERT: V 317 ASP cc_start: 0.7873 (m-30) cc_final: 0.7340 (m-30) REVERT: V 329 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7522 (tm-30) REVERT: V 354 ILE cc_start: 0.7846 (mt) cc_final: 0.7561 (mm) REVERT: V 385 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7278 (mm-30) REVERT: V 394 GLN cc_start: 0.7435 (pt0) cc_final: 0.6993 (pt0) REVERT: V 443 LYS cc_start: 0.7790 (ttpp) cc_final: 0.7448 (ttmm) REVERT: W 36 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7144 (mm110) REVERT: W 42 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8369 (mm-30) REVERT: W 130 LYS cc_start: 0.7911 (ttmm) cc_final: 0.7705 (ttpp) REVERT: W 181 LYS cc_start: 0.7654 (ttpp) cc_final: 0.7359 (ttmt) REVERT: W 182 GLU cc_start: 0.7474 (tp30) cc_final: 0.6943 (tm-30) REVERT: W 198 LYS cc_start: 0.8352 (tttt) cc_final: 0.8074 (tttt) REVERT: W 208 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6645 (ttt-90) REVERT: W 220 ARG cc_start: 0.7255 (mpp80) cc_final: 0.6973 (mpp80) REVERT: W 283 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6796 (tm-30) REVERT: W 285 LYS cc_start: 0.8067 (ttmm) cc_final: 0.7734 (ttpp) REVERT: W 338 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8264 (mttp) REVERT: W 385 ASP cc_start: 0.7194 (m-30) cc_final: 0.6748 (m-30) REVERT: W 389 LYS cc_start: 0.7576 (mmmm) cc_final: 0.7177 (mmmm) REVERT: W 393 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6408 (mt-10) REVERT: W 413 ARG cc_start: 0.7821 (mtm180) cc_final: 0.7298 (ptp90) REVERT: W 419 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6597 (mp0) REVERT: W 421 GLU cc_start: 0.7822 (pm20) cc_final: 0.7600 (mp0) REVERT: W 425 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7380 (ttt90) REVERT: W 455 GLN cc_start: 0.7278 (mm110) cc_final: 0.7072 (tt0) REVERT: X 37 GLU cc_start: 0.7731 (pp20) cc_final: 0.7385 (pp20) REVERT: X 45 GLU cc_start: 0.7117 (tp30) cc_final: 0.6338 (tt0) REVERT: X 94 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.6639 (mp10) REVERT: X 125 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7504 (t80) REVERT: X 134 LYS cc_start: 0.8116 (ptpt) cc_final: 0.7708 (ptpp) REVERT: X 135 GLU cc_start: 0.7200 (tt0) cc_final: 0.6616 (mt-10) REVERT: X 143 GLU cc_start: 0.7667 (tt0) cc_final: 0.7189 (tt0) REVERT: X 150 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7151 (tt0) REVERT: X 156 LEU cc_start: 0.8703 (mt) cc_final: 0.8479 (OUTLIER) REVERT: X 177 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7891 (ttmm) REVERT: X 182 ASP cc_start: 0.8272 (t70) cc_final: 0.7696 (t0) REVERT: X 196 ILE cc_start: 0.8046 (mt) cc_final: 0.7813 (mm) REVERT: X 221 GLU cc_start: 0.7811 (tp30) cc_final: 0.7413 (tp30) REVERT: X 223 ASP cc_start: 0.7813 (m-30) cc_final: 0.7550 (m-30) REVERT: X 229 TYR cc_start: 0.7445 (m-80) cc_final: 0.6991 (m-80) REVERT: X 230 VAL cc_start: 0.8170 (t) cc_final: 0.7751 (p) REVERT: X 232 LEU cc_start: 0.8718 (tp) cc_final: 0.8480 (mm) REVERT: X 242 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7385 (mp0) REVERT: X 243 ILE cc_start: 0.7745 (mt) cc_final: 0.7459 (mp) REVERT: X 264 ASP cc_start: 0.7257 (p0) cc_final: 0.7020 (p0) REVERT: X 282 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6843 (tm-30) REVERT: X 317 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6843 (m-30) REVERT: X 341 ASN cc_start: 0.8466 (p0) cc_final: 0.8224 (p0) REVERT: X 351 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6997 (mm-30) REVERT: X 396 GLU cc_start: 0.6652 (tm-30) cc_final: 0.6126 (tm-30) REVERT: Y 69 ARG cc_start: 0.8138 (mtt90) cc_final: 0.7863 (mmm-85) REVERT: Y 81 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6930 (mtmm) REVERT: Y 106 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7997 (mp) REVERT: Y 130 LYS cc_start: 0.8166 (ttmm) cc_final: 0.7939 (ttpp) REVERT: Y 236 VAL cc_start: 0.8409 (OUTLIER) cc_final: 0.8133 (t) REVERT: Y 272 GLN cc_start: 0.7252 (tt0) cc_final: 0.6900 (tt0) REVERT: Y 282 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7434 (tp30) REVERT: Y 297 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7736 (mm-30) REVERT: Y 350 ARG cc_start: 0.7722 (mtm-85) cc_final: 0.7204 (mtp85) REVERT: Y 357 LYS cc_start: 0.8409 (mttm) cc_final: 0.8089 (mtpp) REVERT: Y 378 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7260 (mt-10) REVERT: Q 1021 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7674 (m-30) REVERT: Q 1030 THR cc_start: 0.7913 (p) cc_final: 0.7301 (p) REVERT: Q 1078 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.7404 (mtm-85) REVERT: Q 1087 ARG cc_start: 0.7748 (mtm110) cc_final: 0.7520 (mtm-85) REVERT: Q 1092 ASP cc_start: 0.7535 (m-30) cc_final: 0.7152 (m-30) REVERT: Q 1103 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.6986 (p0) REVERT: Q 1123 GLU cc_start: 0.7658 (mp0) cc_final: 0.7310 (mp0) REVERT: Q 1134 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7500 (mm-30) REVERT: Q 1160 LYS cc_start: 0.7853 (ptpp) cc_final: 0.7534 (ptpp) REVERT: Q 1176 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6845 (mm-30) REVERT: Q 1189 SER cc_start: 0.7888 (t) cc_final: 0.7484 (p) REVERT: Q 1200 ARG cc_start: 0.7675 (mtm110) cc_final: 0.7275 (mtp85) REVERT: Q 1231 ASN cc_start: 0.7808 (m-40) cc_final: 0.7529 (m-40) REVERT: Q 1239 ASP cc_start: 0.7130 (t0) cc_final: 0.6864 (t70) REVERT: Q 1260 LYS cc_start: 0.8300 (mtpp) cc_final: 0.8047 (mtpp) REVERT: Q 1266 GLU cc_start: 0.7691 (mp0) cc_final: 0.7132 (mp0) REVERT: Q 1280 LYS cc_start: 0.7988 (ptpp) cc_final: 0.7660 (ptpp) REVERT: Q 1316 HIS cc_start: 0.8106 (m-70) cc_final: 0.7434 (m-70) REVERT: Q 1327 MET cc_start: 0.5193 (pmm) cc_final: 0.4489 (pmm) REVERT: Q 1371 LEU cc_start: 0.7305 (mp) cc_final: 0.7088 (pt) REVERT: Q 1405 MET cc_start: 0.6844 (tmm) cc_final: 0.6487 (mmm) REVERT: Z 295 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.8007 (mtpp) outliers start: 98 outliers final: 60 residues processed: 871 average time/residue: 1.7093 time to fit residues: 1704.1365 Evaluate side-chains 904 residues out of total 3167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 820 time to evaluate : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 132 ASN Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 591 LEU Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 147 MET Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 253 ASP Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 160 ILE Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 201 LYS Chi-restraints excluded: chain U residue 239 VAL Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 398 SER Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 131 GLU Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 233 LYS Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 338 LYS Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 241 LYS Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain Y residue 81 LYS Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 238 THR Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 361 GLU Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 440 VAL Chi-restraints excluded: chain Q residue 950 ILE Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1091 GLU Chi-restraints excluded: chain Q residue 1103 ASP Chi-restraints excluded: chain Q residue 1193 VAL Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1389 VAL Chi-restraints excluded: chain Z residue 295 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 0.5980 chunk 305 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 264 optimal weight: 0.0070 chunk 42 optimal weight: 0.5980 chunk 79 optimal weight: 0.0370 chunk 286 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 294 optimal weight: 2.9990 chunk 36 optimal weight: 0.0170 chunk 52 optimal weight: 1.9990 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 65 ASN ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 633 GLN U 248 ASN V 51 GLN V 263 GLN V 417 GLN ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 173 ASN W 360 ASN X 124 ASN X 289 ASN X 325 ASN X 430 ASN Y 49 GLN Y 310 ASN Q1244 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.101294 restraints weight = 43871.809| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.12 r_work: 0.3225 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 29102 Z= 0.159 Angle : 0.582 11.978 39373 Z= 0.281 Chirality : 0.042 0.243 4620 Planarity : 0.003 0.049 5040 Dihedral : 6.328 119.592 4004 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.59 % Allowed : 31.57 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3618 helix: 1.08 (0.14), residues: 1490 sheet: 0.50 (0.20), residues: 638 loop : -0.85 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 280 HIS 0.006 0.001 HIS Y 25 PHE 0.016 0.001 PHE R 691 TYR 0.038 0.001 TYR R 724 ARG 0.012 0.000 ARG S 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21057.30 seconds wall clock time: 368 minutes 7.51 seconds (22087.51 seconds total)