Starting phenix.real_space_refine on Sun Apr 14 17:09:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmp_25998/04_2024/7tmp_25998_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmp_25998/04_2024/7tmp_25998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmp_25998/04_2024/7tmp_25998.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmp_25998/04_2024/7tmp_25998.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmp_25998/04_2024/7tmp_25998_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmp_25998/04_2024/7tmp_25998_updated.pdb" } resolution = 3.3 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= 0.005 sd= 0.139 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 91 5.16 5 C 20533 2.51 5 N 5797 2.21 5 O 5681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 195": "OE1" <-> "OE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 545": "OD1" <-> "OD2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 133": "OD1" <-> "OD2" Residue "D ASP 228": "OD1" <-> "OD2" Residue "D ASP 340": "OD1" <-> "OD2" Residue "D ASP 341": "OD1" <-> "OD2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E GLU 285": "OE1" <-> "OE2" Residue "E GLU 289": "OE1" <-> "OE2" Residue "E PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F GLU 290": "OE1" <-> "OE2" Residue "F GLU 296": "OE1" <-> "OE2" Residue "F TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 398": "OD1" <-> "OD2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "I GLU 127": "OE1" <-> "OE2" Residue "K TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 32105 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4228 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 435 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 30, 'ASN:plan1': 3, 'GLN:plan1': 4, 'ASP:plan': 30} Unresolved non-hydrogen planarities: 242 Chain: "B" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3380 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 24, 'ASN:plan1': 6, 'ARG:plan': 2, 'ASP:plan': 21} Unresolved non-hydrogen planarities: 195 Chain: "C" Number of atoms: 4098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4098 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 561} Unresolved non-hydrogen bonds: 476 Unresolved non-hydrogen angles: 587 Unresolved non-hydrogen dihedrals: 376 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 29, 'TYR:plan': 1, 'ASN:plan1': 8, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 31, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 307 Chain: "D" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3350 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 308 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 25, 'ASN:plan1': 7, 'ARG:plan': 1, 'ASP:plan': 17} Unresolved non-hydrogen planarities: 189 Chain: "E" Number of atoms: 4169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4169 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 559} Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 6, 'ASP:plan': 27, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 248 Chain: "F" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3366 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 290 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 24, 'ARG:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 17} Unresolved non-hydrogen planarities: 175 Chain: "G" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1237 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 5, 'TRANS': 181} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 9, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 152 Chain: "H" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 484 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 94 Chain: "I" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1366 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 5, 'TRANS': 211} Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 225 Chain: "J" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 588 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 1, 'TRANS': 106} Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "K" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1265 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 5, 'TRANS': 190} Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 10, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 21, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 187 Chain: "L" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 486 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 118 Chain: "M" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1316 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 3, 'TRANS': 210} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 259 Chain: "N" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 551 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 454 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 196 Chain: "P" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 2193 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 410} Link IDs: {'PTRANS': 9, 'TRANS': 431} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1426 Unresolved non-hydrogen angles: 1821 Unresolved non-hydrogen dihedrals: 1158 Unresolved non-hydrogen chiralities: 154 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 30, 'TYR:plan': 11, 'ASN:plan1': 24, 'TRP:plan': 5, 'HIS:plan': 10, 'PHE:plan': 15, 'GLU:plan': 32, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 718 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.41, per 1000 atoms: 0.54 Number of scatterers: 32105 At special positions: 0 Unit cell: (134.93, 139.05, 203.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 91 16.00 P 2 15.00 Mg 1 11.99 O 5681 8.00 N 5797 7.00 C 20533 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=0, symmetry=0 Time building additional restraints: 13.70 Conformation dependent library (CDL) restraints added in 6.6 seconds 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8972 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 159 helices and 33 sheets defined 49.0% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.14 Creating SS restraints... Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 287 through 299 Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 311 through 314 Processing helix chain 'A' and resid 326 through 345 removed outlier: 3.792A pdb=" N GLU A 330 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 Processing helix chain 'A' and resid 384 through 393 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 426 through 434 Processing helix chain 'A' and resid 443 through 449 removed outlier: 4.870A pdb=" N ARG A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 474 removed outlier: 4.590A pdb=" N LYS A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 502 Processing helix chain 'A' and resid 509 through 524 Processing helix chain 'A' and resid 540 through 562 Processing helix chain 'A' and resid 567 through 586 removed outlier: 5.615A pdb=" N ASP A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N PHE A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 593 through 615 Processing helix chain 'B' and resid 15 through 19 removed outlier: 3.655A pdb=" N GLY B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 15 through 19' Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 180 through 190 Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 252 through 268 Proline residue: B 256 - end of helix Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 306 through 318 removed outlier: 4.335A pdb=" N TYR B 309 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU B 317 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 318 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 396 through 420 Processing helix chain 'B' and resid 427 through 442 Processing helix chain 'B' and resid 454 through 466 Processing helix chain 'B' and resid 478 through 484 Processing helix chain 'C' and resid 112 through 119 Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 262 through 271 Processing helix chain 'C' and resid 287 through 299 Proline residue: C 298 - end of helix Processing helix chain 'C' and resid 311 through 314 Processing helix chain 'C' and resid 326 through 345 removed outlier: 4.793A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 371 Processing helix chain 'C' and resid 384 through 393 Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 426 through 434 Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 464 through 474 removed outlier: 4.811A pdb=" N LYS C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 501 Processing helix chain 'C' and resid 509 through 524 Processing helix chain 'C' and resid 540 through 563 Processing helix chain 'C' and resid 567 through 583 removed outlier: 5.615A pdb=" N ASP C 576 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL C 577 " --> pdb=" O SER C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 614 Processing helix chain 'D' and resid 17 through 19 No H-bonds generated for 'chain 'D' and resid 17 through 19' Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 141 through 143 No H-bonds generated for 'chain 'D' and resid 141 through 143' Processing helix chain 'D' and resid 156 through 161 Processing helix chain 'D' and resid 180 through 190 Processing helix chain 'D' and resid 219 through 232 Processing helix chain 'D' and resid 234 through 237 removed outlier: 3.770A pdb=" N ARG D 237 " --> pdb=" O SER D 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 234 through 237' Processing helix chain 'D' and resid 249 through 270 Proline residue: D 256 - end of helix Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 308 through 317 Processing helix chain 'D' and resid 345 through 353 Processing helix chain 'D' and resid 362 through 367 removed outlier: 3.666A pdb=" N LYS D 367 " --> pdb=" O GLN D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 386 No H-bonds generated for 'chain 'D' and resid 383 through 386' Processing helix chain 'D' and resid 396 through 420 removed outlier: 4.184A pdb=" N ALA D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 442 removed outlier: 3.795A pdb=" N SER D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 467 removed outlier: 4.263A pdb=" N ILE D 467 " --> pdb=" O SER D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 484 Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 260 through 272 removed outlier: 4.077A pdb=" N GLN E 267 " --> pdb=" O THR E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.601A pdb=" N VAL E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 314 Processing helix chain 'E' and resid 326 through 345 removed outlier: 4.404A pdb=" N ILE E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 371 Processing helix chain 'E' and resid 382 through 394 removed outlier: 4.226A pdb=" N GLY E 385 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU E 393 " --> pdb=" O SER E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 434 Processing helix chain 'E' and resid 443 through 447 Processing helix chain 'E' and resid 464 through 474 removed outlier: 4.417A pdb=" N LYS E 469 " --> pdb=" O ASN E 465 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE E 470 " --> pdb=" O VAL E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 502 Processing helix chain 'E' and resid 509 through 524 Processing helix chain 'E' and resid 540 through 563 Processing helix chain 'E' and resid 567 through 583 removed outlier: 5.633A pdb=" N ASP E 576 " --> pdb=" O ASP E 572 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL E 577 " --> pdb=" O SER E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 593 through 612 removed outlier: 3.700A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE E 611 " --> pdb=" O MET E 607 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA E 612 " --> pdb=" O GLN E 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 19 No H-bonds generated for 'chain 'F' and resid 17 through 19' Processing helix chain 'F' and resid 141 through 143 No H-bonds generated for 'chain 'F' and resid 141 through 143' Processing helix chain 'F' and resid 156 through 159 No H-bonds generated for 'chain 'F' and resid 156 through 159' Processing helix chain 'F' and resid 180 through 189 Processing helix chain 'F' and resid 219 through 232 Processing helix chain 'F' and resid 251 through 268 Proline residue: F 256 - end of helix Processing helix chain 'F' and resid 281 through 294 Processing helix chain 'F' and resid 306 through 318 removed outlier: 4.269A pdb=" N TYR F 309 " --> pdb=" O GLY F 306 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 312 " --> pdb=" O TYR F 309 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR F 316 " --> pdb=" O SER F 313 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU F 317 " --> pdb=" O THR F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 353 Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 383 through 386 No H-bonds generated for 'chain 'F' and resid 383 through 386' Processing helix chain 'F' and resid 396 through 419 Processing helix chain 'F' and resid 422 through 424 No H-bonds generated for 'chain 'F' and resid 422 through 424' Processing helix chain 'F' and resid 427 through 442 Processing helix chain 'F' and resid 454 through 467 removed outlier: 3.918A pdb=" N ILE F 467 " --> pdb=" O SER F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 472 No H-bonds generated for 'chain 'F' and resid 470 through 472' Processing helix chain 'F' and resid 478 through 484 Processing helix chain 'G' and resid 46 through 112 removed outlier: 3.532A pdb=" N GLU G 105 " --> pdb=" O GLU G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 132 removed outlier: 3.641A pdb=" N LYS G 118 " --> pdb=" O ARG G 114 " (cutoff:3.500A) Proline residue: G 119 - end of helix removed outlier: 3.541A pdb=" N LYS G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 163 removed outlier: 5.527A pdb=" N ASP G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 213 Processing helix chain 'G' and resid 215 through 222 Processing helix chain 'H' and resid 30 through 103 removed outlier: 3.787A pdb=" N ILE H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU H 82 " --> pdb=" O GLY H 78 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 113 Processing helix chain 'I' and resid 117 through 130 Processing helix chain 'I' and resid 146 through 163 removed outlier: 5.587A pdb=" N ASP I 154 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASP I 155 " --> pdb=" O SER I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 213 Processing helix chain 'I' and resid 215 through 222 Processing helix chain 'J' and resid 6 through 62 Processing helix chain 'J' and resid 65 through 103 removed outlier: 3.735A pdb=" N ALA J 72 " --> pdb=" O LEU J 68 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU J 73 " --> pdb=" O GLU J 69 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 112 removed outlier: 3.585A pdb=" N ALA K 111 " --> pdb=" O LEU K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 132 Proline residue: K 119 - end of helix Processing helix chain 'K' and resid 146 through 151 Processing helix chain 'K' and resid 153 through 163 Processing helix chain 'K' and resid 203 through 213 Processing helix chain 'K' and resid 215 through 221 Processing helix chain 'L' and resid 26 through 67 Processing helix chain 'L' and resid 70 through 103 removed outlier: 5.949A pdb=" N ASP L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ASP L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 75 Processing helix chain 'M' and resid 80 through 85 Processing helix chain 'M' and resid 129 through 216 removed outlier: 4.831A pdb=" N ILE M 178 " --> pdb=" O GLU M 174 " (cutoff:3.500A) Proline residue: M 179 - end of helix Processing helix chain 'N' and resid 14 through 23 Processing helix chain 'N' and resid 47 through 58 Processing helix chain 'N' and resid 71 through 76 removed outlier: 3.749A pdb=" N ASN N 76 " --> pdb=" O HIS N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 83 Processing helix chain 'N' and resid 107 through 111 removed outlier: 3.687A pdb=" N ARG N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 107 through 111' Processing helix chain 'P' and resid 11 through 22 Processing helix chain 'P' and resid 27 through 32 Processing helix chain 'P' and resid 38 through 50 Processing helix chain 'P' and resid 74 through 86 removed outlier: 3.599A pdb=" N ILE P 78 " --> pdb=" O LYS P 75 " (cutoff:3.500A) Proline residue: P 79 - end of helix Processing helix chain 'P' and resid 90 through 105 Processing helix chain 'P' and resid 111 through 119 Processing helix chain 'P' and resid 121 through 130 Processing helix chain 'P' and resid 136 through 151 Processing helix chain 'P' and resid 158 through 166 Processing helix chain 'P' and resid 168 through 175 Processing helix chain 'P' and resid 180 through 195 removed outlier: 4.095A pdb=" N VAL P 195 " --> pdb=" O GLN P 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 209 Processing helix chain 'P' and resid 211 through 222 Processing helix chain 'P' and resid 238 through 255 Processing helix chain 'P' and resid 257 through 266 removed outlier: 3.567A pdb=" N GLN P 265 " --> pdb=" O ASN P 261 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 280 Processing helix chain 'P' and resid 284 through 298 Processing helix chain 'P' and resid 305 through 315 Processing helix chain 'P' and resid 318 through 327 Processing helix chain 'P' and resid 333 through 352 removed outlier: 3.767A pdb=" N GLU P 352 " --> pdb=" O ASN P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 365 Processing helix chain 'P' and resid 372 through 375 No H-bonds generated for 'chain 'P' and resid 372 through 375' Processing helix chain 'P' and resid 377 through 410 removed outlier: 5.044A pdb=" N ASP P 385 " --> pdb=" O SER P 381 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLU P 386 " --> pdb=" O ASP P 382 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ASP P 390 " --> pdb=" O GLU P 386 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN P 391 " --> pdb=" O PHE P 387 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE P 394 " --> pdb=" O ASP P 390 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE P 395 " --> pdb=" O ASN P 391 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP P 410 " --> pdb=" O VAL P 406 " (cutoff:3.500A) Processing helix chain 'P' and resid 414 through 432 Processing helix chain 'P' and resid 435 through 443 Processing helix chain 'P' and resid 446 through 455 removed outlier: 3.781A pdb=" N ASN P 455 " --> pdb=" O MET P 451 " (cutoff:3.500A) Processing helix chain 'P' and resid 459 through 472 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.667A pdb=" N LYS A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 62 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN A 71 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL A 60 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 93 through 96 Processing sheet with id= C, first strand: chain 'A' and resid 189 through 191 removed outlier: 6.950A pdb=" N ILE A 172 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER A 160 " --> pdb=" O HIS A 170 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N HIS A 170 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 251 through 253 removed outlier: 8.012A pdb=" N THR A 252 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE A 412 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA A 277 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE A 353 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE A 279 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 181 through 185 removed outlier: 6.711A pdb=" N GLU A 199 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE A 185 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 197 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE A 209 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU A 199 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N SER A 207 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU A 201 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LYS A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 92 through 95 removed outlier: 5.853A pdb=" N GLU B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL B 31 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 101 through 104 Processing sheet with id= H, first strand: chain 'B' and resid 171 through 173 Processing sheet with id= I, first strand: chain 'B' and resid 320 through 322 removed outlier: 3.767A pdb=" N ILE B 329 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL B 322 " --> pdb=" O GLY B 327 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY B 327 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 211 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N THR B 279 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA B 213 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N SER B 239 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA B 214 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE B 241 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY B 216 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASN B 243 " --> pdb=" O GLY B 216 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 26 through 31 removed outlier: 6.436A pdb=" N ILE C 36 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL C 30 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN C 71 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL C 60 " --> pdb=" O GLN C 71 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 93 through 96 Processing sheet with id= L, first strand: chain 'C' and resid 189 through 192 removed outlier: 3.509A pdb=" N TRP C 139 " --> pdb=" O TYR C 191 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLN C 140 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 172 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N SER C 160 " --> pdb=" O HIS C 170 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N HIS C 170 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 207 through 209 removed outlier: 3.753A pdb=" N SER C 207 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLU C 201 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE C 182 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 251 through 254 removed outlier: 8.296A pdb=" N THR C 252 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE C 412 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE C 254 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA C 414 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA C 277 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE C 353 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE C 279 " --> pdb=" O ILE C 353 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 31 through 35 removed outlier: 6.866A pdb=" N ILE D 40 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL D 34 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU D 38 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA D 75 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU D 69 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLN D 78 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL D 67 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 101 through 104 removed outlier: 3.668A pdb=" N ASP D 130 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 171 through 173 Processing sheet with id= R, first strand: chain 'D' and resid 239 through 242 Processing sheet with id= S, first strand: chain 'E' and resid 26 through 31 removed outlier: 6.479A pdb=" N ILE E 36 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL E 30 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN E 71 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL E 60 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 93 through 96 Processing sheet with id= U, first strand: chain 'E' and resid 189 through 191 Processing sheet with id= V, first strand: chain 'E' and resid 409 through 414 removed outlier: 7.242A pdb=" N ALA E 277 " --> pdb=" O SER E 351 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE E 353 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE E 279 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASP E 355 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL E 281 " --> pdb=" O ASP E 355 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL E 318 " --> pdb=" O GLY E 282 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLY E 284 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASN E 320 " --> pdb=" O GLY E 284 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 398 through 400 removed outlier: 4.488A pdb=" N ARG E 406 " --> pdb=" O ALA E 400 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 182 through 185 removed outlier: 6.683A pdb=" N GLU E 199 " --> pdb=" O THR E 183 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE E 185 " --> pdb=" O ILE E 197 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE E 197 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE E 209 " --> pdb=" O ILE E 197 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU E 199 " --> pdb=" O SER E 207 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER E 207 " --> pdb=" O GLU E 199 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 26 through 28 removed outlier: 4.051A pdb=" N LEU F 26 " --> pdb=" O PHE F 95 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE F 76 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 101 through 104 Processing sheet with id= AA, first strand: chain 'F' and resid 111 through 113 removed outlier: 3.658A pdb=" N ARG F 111 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE F 210 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE F 241 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE F 212 " --> pdb=" O PHE F 241 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASN F 243 " --> pdb=" O PHE F 212 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ALA F 214 " --> pdb=" O ASN F 243 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 357 through 359 Processing sheet with id= AC, first strand: chain 'G' and resid 171 through 174 Processing sheet with id= AD, first strand: chain 'I' and resid 171 through 174 removed outlier: 4.181A pdb=" N VAL I 188 " --> pdb=" O ASN I 201 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 171 through 174 Processing sheet with id= AF, first strand: chain 'M' and resid 92 through 98 Processing sheet with id= AG, first strand: chain 'N' and resid 8 through 10 removed outlier: 6.198A pdb=" N ILE N 66 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA N 90 " --> pdb=" O LEU N 67 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG 1880 hydrogen bonds defined for protein. 5394 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: 12.42 Time building geometry restraints manager: 14.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 5233 1.30 - 1.43: 7900 1.43 - 1.56: 19340 1.56 - 1.68: 3 1.68 - 1.81: 165 Bond restraints: 32641 Sorted by residual: bond pdb=" C ARG G 206 " pdb=" O ARG G 206 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.26e-02 6.30e+03 2.34e+01 bond pdb=" C ASP F 159 " pdb=" O ASP F 159 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.15e-02 7.56e+03 1.63e+01 bond pdb=" CA GLY I 187 " pdb=" C GLY I 187 " ideal model delta sigma weight residual 1.516 1.461 0.055 1.37e-02 5.33e+03 1.62e+01 bond pdb=" C LEU C 48 " pdb=" O LEU C 48 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.21e-02 6.83e+03 1.52e+01 bond pdb=" C VAL H 102 " pdb=" O VAL H 102 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.17e-02 7.31e+03 1.49e+01 ... (remaining 32636 not shown) Histogram of bond angle deviations from ideal: 98.51 - 105.99: 765 105.99 - 113.48: 18485 113.48 - 120.96: 16244 120.96 - 128.45: 9086 128.45 - 135.93: 121 Bond angle restraints: 44701 Sorted by residual: angle pdb=" N THR F 160 " pdb=" CA THR F 160 " pdb=" C THR F 160 " ideal model delta sigma weight residual 111.28 118.15 -6.87 1.09e+00 8.42e-01 3.97e+01 angle pdb=" N VAL H 102 " pdb=" CA VAL H 102 " pdb=" C VAL H 102 " ideal model delta sigma weight residual 110.62 106.18 4.44 1.02e+00 9.61e-01 1.89e+01 angle pdb=" N GLY A 89 " pdb=" CA GLY A 89 " pdb=" C GLY A 89 " ideal model delta sigma weight residual 115.32 109.62 5.70 1.38e+00 5.25e-01 1.70e+01 angle pdb=" N THR H 101 " pdb=" CA THR H 101 " pdb=" C THR H 101 " ideal model delta sigma weight residual 111.69 116.42 -4.73 1.23e+00 6.61e-01 1.48e+01 angle pdb=" N ARG C 359 " pdb=" CA ARG C 359 " pdb=" C ARG C 359 " ideal model delta sigma weight residual 111.28 107.43 3.85 1.09e+00 8.42e-01 1.25e+01 ... (remaining 44696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18128 17.98 - 35.96: 1043 35.96 - 53.94: 188 53.94 - 71.91: 23 71.91 - 89.89: 16 Dihedral angle restraints: 19398 sinusoidal: 5499 harmonic: 13899 Sorted by residual: dihedral pdb=" CA LYS B 384 " pdb=" C LYS B 384 " pdb=" N SER B 385 " pdb=" CA SER B 385 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LEU C 100 " pdb=" C LEU C 100 " pdb=" N MET C 101 " pdb=" CA MET C 101 " ideal model delta harmonic sigma weight residual 180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ALA B 386 " pdb=" C ALA B 386 " pdb=" N ILE B 387 " pdb=" CA ILE B 387 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 19395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4800 0.061 - 0.122: 674 0.122 - 0.183: 37 0.183 - 0.244: 4 0.244 - 0.306: 2 Chirality restraints: 5517 Sorted by residual: chirality pdb=" CA MET F 161 " pdb=" N MET F 161 " pdb=" C MET F 161 " pdb=" CB MET F 161 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA THR F 160 " pdb=" N THR F 160 " pdb=" C THR F 160 " pdb=" CB THR F 160 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA THR C 88 " pdb=" N THR C 88 " pdb=" C THR C 88 " pdb=" CB THR C 88 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 5514 not shown) Planarity restraints: 5807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 477 " 0.048 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO D 478 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 478 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 478 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 184 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C VAL I 184 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL I 184 " 0.016 2.00e-02 2.50e+03 pdb=" N SER I 185 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 100 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C GLU H 100 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU H 100 " -0.015 2.00e-02 2.50e+03 pdb=" N THR H 101 " -0.014 2.00e-02 2.50e+03 ... (remaining 5804 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 205 2.57 - 3.15: 27019 3.15 - 3.74: 53655 3.74 - 4.32: 68926 4.32 - 4.90: 118936 Nonbonded interactions: 268741 Sorted by model distance: nonbonded pdb=" O2B ADP A 701 " pdb="MG MG A 702 " model vdw 1.989 2.170 nonbonded pdb=" OG1 THR A 263 " pdb="MG MG A 702 " model vdw 2.019 2.170 nonbonded pdb=" O TYR B 468 " pdb=" OH TYR B 485 " model vdw 2.198 2.440 nonbonded pdb=" O TYR F 468 " pdb=" OH TYR F 485 " model vdw 2.212 2.440 nonbonded pdb=" NZ LYS B 169 " pdb=" OE2 GLU B 355 " model vdw 2.231 2.520 ... (remaining 268736 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 'A' and (resid 24 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 54 or (resid 55 and (name N or nam \ e CA or name C or name O or name CB )) or resid 56 through 89 or (resid 90 and ( \ name N or name CA or name C or name O or name CB )) or resid 91 through 112 or ( \ resid 113 through 114 and (name N or name CA or name C or name O or name CB )) o \ r resid 115 through 116 or (resid 117 through 121 and (name N or name CA or name \ C or name O or name CB )) or resid 122 through 125 or (resid 126 and (name N or \ name CA or name C or name O or name CB )) or resid 127 through 129 or (resid 13 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 131 through \ 147 or (resid 148 and (name N or name CA or name C or name O or name CB )) or re \ sid 149 through 177 or (resid 178 and (name N or name CA or name C or name O or \ name CB )) or resid 179 through 180 or (resid 181 and (name N or name CA or name \ C or name O or name CB )) or resid 182 or (resid 183 and (name N or name CA or \ name C or name O or name CB )) or resid 184 through 189 or (resid 190 and (name \ N or name CA or name C or name O or name CB )) or resid 191 through 194 or (resi \ d 195 and (name N or name CA or name C or name O or name CB )) or resid 196 thro \ ugh 205 or (resid 206 through 208 and (name N or name CA or name C or name O or \ name CB )) or resid 209 through 234 or (resid 235 and (name N or name CA or name \ C or name O or name CB )) or resid 236 through 240 or (resid 241 through 242 an \ d (name N or name CA or name C or name O or name CB )) or resid 243 through 257 \ or (resid 258 and (name N or name CA or name C or name O or name CB )) or resid \ 259 or (resid 260 and (name N or name CA or name C or name O or name CB )) or re \ sid 261 or (resid 262 through 266 and (name N or name CA or name C or name O or \ name CB )) or resid 267 through 268 or (resid 269 through 271 and (name N or nam \ e CA or name C or name O or name CB )) or resid 272 or (resid 273 through 277 an \ d (name N or name CA or name C or name O or name CB )) or resid 278 through 288 \ or (resid 289 and (name N or name CA or name C or name O or name CB )) or resid \ 290 through 294 or (resid 295 through 296 and (name N or name CA or name C or na \ me O or name CB )) or resid 297 through 310 or (resid 311 and (name N or name CA \ or name C or name O or name CB )) or resid 312 through 314 or (resid 315 and (n \ ame N or name CA or name C or name O or name CB )) or resid 316 through 329 or ( \ resid 330 through 332 and (name N or name CA or name C or name O or name CB )) o \ r resid 333 through 372 or (resid 373 and (name N or name CA or name C or name O \ or name CB )) or resid 374 through 377 or (resid 378 and (name N or name CA or \ name C or name O or name CB )) or resid 379 through 389 or (resid 390 and (name \ N or name CA or name C or name O or name CB )) or resid 391 through 406 or (resi \ d 407 and (name N or name CA or name C or name O or name CB )) or resid 408 or ( \ resid 409 and (name N or name CA or name C or name O or name CB )) or resid 410 \ through 416 or (resid 417 and (name N or name CA or name C or name O or name CB \ )) or resid 418 through 422 or (resid 423 through 425 and (name N or name CA or \ name C or name O or name CB )) or resid 426 through 442 or (resid 443 through 44 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 445 through \ 446 or (resid 447 through 451 and (name N or name CA or name C or name O or name \ CB )) or resid 452 or (resid 453 and (name N or name CA or name C or name O or \ name CB )) or resid 454 or (resid 455 through 459 and (name N or name CA or name \ C or name O or name CB )) or resid 460 or (resid 461 and (name N or name CA or \ name C or name O or name CB )) or resid 462 through 464 or (resid 465 and (name \ N or name CA or name C or name O or name CB )) or resid 466 through 473 or (resi \ d 474 and (name N or name CA or name C or name O or name CB )) or resid 475 thro \ ugh 482 or (resid 483 and (name N or name CA or name C or name O or name CB )) o \ r resid 484 through 490 or (resid 491 through 502 and (name N or name CA or name \ C or name O or name CB )) or resid 503 through 509 or (resid 510 through 512 an \ d (name N or name CA or name C or name O or name CB )) or resid 513 through 528 \ or (resid 529 and (name N or name CA or name C or name O or name CB )) or resid \ 530 or (resid 531 through 533 and (name N or name CA or name C or name O or name \ CB )) or resid 534 through 537 or (resid 538 and (name N or name CA or name C o \ r name O or name CB )) or resid 539 through 544 or (resid 545 and (name N or nam \ e CA or name C or name O or name CB )) or resid 546 or (resid 547 and (name N or \ name CA or name C or name O or name CB )) or resid 548 through 557 or (resid 55 \ 8 through 563 and (name N or name CA or name C or name O or name CB )) or resid \ 564 through 569 or (resid 570 through 574 and (name N or name CA or name C or na \ me O or name CB )) or resid 575 through 578 or (resid 579 through 580 and (name \ N or name CA or name C or name O or name CB )) or resid 581 or (resid 582 throug \ h 584 and (name N or name CA or name C or name O or name CB )) or resid 585 thro \ ugh 587 or (resid 588 and (name N or name CA or name C or name O or name CB )) o \ r resid 589 or (resid 590 through 591 and (name N or name CA or name C or name O \ or name CB )) or resid 592 through 602 or (resid 603 and (name N or name CA or \ name C or name O or name CB )) or resid 604 through 606 or (resid 607 through 61 \ 3 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and ((resid 24 and (name N or name CA or name C or name O or name CB \ )) or resid 25 through 35 or (resid 36 through 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 or (resid 41 and (name N or name CA or na \ me C or name O or name CB )) or resid 42 or (resid 43 through 44 and (name N or \ name CA or name C or name O or name CB )) or resid 45 through 50 or (resid 51 an \ d (name N or name CA or name C or name O or name CB )) or resid 52 through 58 or \ (resid 59 and (name N or name CA or name C or name O or name CB )) or resid 60 \ through 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) \ or resid 84 through 92 or (resid 93 and (name N or name CA or name C or name O \ or name CB )) or resid 94 through 107 or (resid 108 and (name N or name CA or na \ me C or name O or name CB )) or resid 109 through 118 or (resid 119 through 121 \ and (name N or name CA or name C or name O or name CB )) or resid 122 through 12 \ 5 or (resid 126 and (name N or name CA or name C or name O or name CB )) or resi \ d 127 through 129 or (resid 130 and (name N or name CA or name C or name O or na \ me CB )) or resid 131 through 139 or (resid 140 and (name N or name CA or name C \ or name O or name CB )) or resid 141 through 147 or (resid 148 and (name N or n \ ame CA or name C or name O or name CB )) or resid 149 through 159 or (resid 160 \ and (name N or name CA or name C or name O or name CB )) or resid 161 through 16 \ 2 or (resid 163 and (name N or name CA or name C or name O or name CB )) or resi \ d 164 or (resid 165 and (name N or name CA or name C or name O or name CB )) or \ resid 166 through 167 or (resid 168 through 169 and (name N or name CA or name C \ or name O or name CB )) or resid 170 through 177 or (resid 178 and (name N or n \ ame CA or name C or name O or name CB )) or resid 179 through 180 or (resid 181 \ and (name N or name CA or name C or name O or name CB )) or resid 182 or (resid \ 183 and (name N or name CA or name C or name O or name CB )) or resid 184 throug \ h 189 or (resid 190 and (name N or name CA or name C or name O or name CB )) or \ resid 191 through 234 or (resid 235 and (name N or name CA or name C or name O o \ r name CB )) or resid 236 through 240 or (resid 241 through 242 and (name N or n \ ame CA or name C or name O or name CB )) or resid 243 through 250 or (resid 251 \ and (name N or name CA or name C or name O or name CB )) or resid 252 through 25 \ 7 or (resid 258 and (name N or name CA or name C or name O or name CB )) or (res \ id 259 through 266 and (name N or name CA or name C or name O or name CB )) or r \ esid 267 or (resid 268 through 271 and (name N or name CA or name C or name O or \ name CB )) or resid 272 through 273 or (resid 274 through 277 and (name N or na \ me CA or name C or name O or name CB )) or resid 278 through 291 or (resid 292 a \ nd (name N or name CA or name C or name O or name CB )) or resid 293 through 356 \ or (resid 357 and (name N or name CA or name C or name O or name CB )) or resid \ 358 through 392 or (resid 393 and (name N or name CA or name C or name O or nam \ e CB )) or resid 394 through 408 or (resid 409 and (name N or name CA or name C \ or name O or name CB )) or resid 410 or (resid 411 and (name N or name CA or nam \ e C or name O or name CB )) or resid 412 through 415 or (resid 416 through 417 a \ nd (name N or name CA or name C or name O or name CB )) or resid 418 through 422 \ or (resid 423 through 425 and (name N or name CA or name C or name O or name CB \ )) or resid 426 through 452 or (resid 453 and (name N or name CA or name C or n \ ame O or name CB )) or resid 454 through 457 or (resid 458 through 459 and (name \ N or name CA or name C or name O or name CB )) or resid 460 through 489 or (res \ id 490 through 502 and (name N or name CA or name C or name O or name CB )) or r \ esid 503 through 537 or (resid 538 and (name N or name CA or name C or name O or \ name CB )) or resid 539 through 544 or (resid 545 and (name N or name CA or nam \ e C or name O or name CB )) or resid 546 through 613)) selection = (chain 'E' and ((resid 24 and (name N or name CA or name C or name O or name CB \ )) or resid 25 through 28 or (resid 29 and (name N or name CA or name C or name \ O or name CB )) or resid 30 or (resid 31 and (name N or name CA or name C or nam \ e O or name CB )) or resid 32 through 35 or (resid 36 through 39 and (name N or \ name CA or name C or name O or name CB )) or resid 40 or (resid 41 and (name N o \ r name CA or name C or name O or name CB )) or resid 42 or (resid 43 through 44 \ and (name N or name CA or name C or name O or name CB )) or resid 45 through 50 \ or (resid 51 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 2 through 53 or (resid 54 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 65 or (resid 66 and (name N or name CA or name \ C or name O or name CB )) or resid 67 through 82 or (resid 83 and (name N or na \ me CA or name C or name O or name CB )) or resid 84 through 92 or (resid 93 and \ (name N or name CA or name C or name O or name CB )) or resid 94 through 107 or \ (resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 112 or (resid 113 through 114 and (name N or name CA or name C or name \ O or name CB )) or resid 115 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 139 or (resid 140 and (name \ N or name CA or name C or name O or name CB )) or resid 141 through 162 or (res \ id 163 and (name N or name CA or name C or name O or name CB )) or resid 164 thr \ ough 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) \ or resid 196 through 205 or (resid 206 through 208 and (name N or name CA or nam \ e C or name O or name CB )) or resid 209 through 250 or (resid 251 and (name N o \ r name CA or name C or name O or name CB )) or resid 252 through 275 or (resid 2 \ 76 through 277 and (name N or name CA or name C or name O or name CB )) or resid \ 278 through 284 or (resid 285 and (name N or name CA or name C or name O or nam \ e CB )) or resid 286 through 288 or (resid 289 and (name N or name CA or name C \ or name O or name CB )) or resid 290 through 301 or (resid 302 through 305 and ( \ name N or name CA or name C or name O or name CB )) or resid 306 through 310 or \ (resid 311 and (name N or name CA or name C or name O or name CB )) or resid 312 \ through 314 or (resid 315 and (name N or name CA or name C or name O or name CB \ )) or resid 316 through 331 or (resid 332 and (name N or name CA or name C or n \ ame O or name CB )) or resid 333 through 356 or (resid 357 and (name N or name C \ A or name C or name O or name CB )) or resid 358 through 365 or (resid 366 and ( \ name N or name CA or name C or name O or name CB )) or resid 367 or (resid 368 a \ nd (name N or name CA or name C or name O or name CB )) or resid 369 through 372 \ or (resid 373 and (name N or name CA or name C or name O or name CB )) or resid \ 374 through 377 or (resid 378 and (name N or name CA or name C or name O or nam \ e CB )) or resid 379 through 406 or (resid 407 and (name N or name CA or name C \ or name O or name CB )) or resid 408 through 415 or (resid 416 through 417 and ( \ name N or name CA or name C or name O or name CB )) or resid 418 through 423 or \ (resid 424 through 425 and (name N or name CA or name C or name O or name CB )) \ or resid 426 through 446 or (resid 447 through 451 and (name N or name CA or nam \ e C or name O or name CB )) or resid 452 through 454 or (resid 455 through 459 a \ nd (name N or name CA or name C or name O or name CB )) or resid 460 through 486 \ or (resid 487 and (name N or name CA or name C or name O or name CB )) or resid \ 488 through 489 or (resid 490 through 502 and (name N or name CA or name C or n \ ame O or name CB )) or resid 503 through 509 or (resid 510 through 512 and (name \ N or name CA or name C or name O or name CB )) or resid 513 through 530 or (res \ id 531 through 533 and (name N or name CA or name C or name O or name CB )) or r \ esid 534 through 546 or (resid 547 and (name N or name CA or name C or name O or \ name CB )) or resid 548 through 551 or (resid 552 and (name N or name CA or nam \ e C or name O or name CB )) or resid 553 through 557 or (resid 558 through 563 a \ nd (name N or name CA or name C or name O or name CB )) or resid 564 through 569 \ or (resid 570 through 574 and (name N or name CA or name C or name O or name CB \ )) or (resid 575 through 577 and (name N or name CA or name C or name O or name \ CB )) or resid 578 or (resid 579 through 580 and (name N or name CA or name C o \ r name O or name CB )) or resid 581 through 583 or (resid 584 and (name N or nam \ e CA or name C or name O or name CB )) or resid 585 through 589 or (resid 590 th \ rough 591 and (name N or name CA or name C or name O or name CB )) or resid 592 \ through 602 or (resid 603 and (name N or name CA or name C or name O or name CB \ )) or resid 604 through 605 or (resid 606 through 613 and (name N or name CA or \ name C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 15 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 60 or (resid 61 and (name N or nam \ e CA or name C or name O or name CB )) or resid 62 through 88 or (resid 89 throu \ gh 90 and (name N or name CA or name C or name O or name CB )) or resid 91 throu \ gh 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or r \ esid 100 through 104 or (resid 105 through 107 and (name N or name CA or name C \ or name O or name CB )) or resid 108 through 136 or (resid 137 and (name N or na \ me CA or name C or name O or name CB )) or resid 138 through 161 or (resid 162 a \ nd (name N or name CA or name C or name O or name CB )) or resid 163 through 173 \ or (resid 174 through 176 and (name N or name CA or name C or name O or name CB \ )) or resid 177 through 194 or (resid 207 and (name N or name CA or name C or n \ ame O or name CB )) or resid 208 or (resid 209 and (name N or name CA or name C \ or name O or name CB )) or resid 210 through 220 or (resid 221 through 222 and ( \ name N or name CA or name C or name O or name CB )) or resid 223 through 226 or \ (resid 227 and (name N or name CA or name C or name O or name CB )) or resid 228 \ through 230 or (resid 231 through 232 and (name N or name CA or name C or name \ O or name CB )) or resid 233 or (resid 234 and (name N or name CA or name C or n \ ame O or name CB )) or resid 235 through 238 or (resid 239 and (name N or name C \ A or name C or name O or name CB )) or resid 240 through 250 or (resid 251 and ( \ name N or name CA or name C or name O or name CB )) or resid 252 through 270 or \ (resid 271 and (name N or name CA or name C or name O or name CB )) or resid 272 \ through 296 or (resid 297 and (name N or name CA or name C or name O or name CB \ )) or resid 298 through 300 or (resid 301 and (name N or name CA or name C or n \ ame O or name CB )) or resid 302 through 312 or (resid 313 and (name N or name C \ A or name C or name O or name CB )) or resid 314 through 316 or (resid 317 and ( \ name N or name CA or name C or name O or name CB )) or resid 318 through 325 or \ (resid 326 and (name N or name CA or name C or name O or name CB )) or resid 327 \ through 377 or (resid 378 and (name N or name CA or name C or name O or name CB \ )) or resid 379 or (resid 380 and (name N or name CA or name C or name O or nam \ e CB )) or resid 381 through 383 or (resid 384 through 387 and (name N or name C \ A or name C or name O or name CB )) or (resid 388 through 392 and (name N or nam \ e CA or name C or name O or name CB )) or resid 393 through 399 or (resid 400 th \ rough 401 and (name N or name CA or name C or name O or name CB )) or resid 402 \ through 416 or (resid 417 through 420 and (name N or name CA or name C or name O \ or name CB )) or (resid 421 through 430 and (name N or name CA or name C or nam \ e O or name CB )) or resid 431 through 437 or (resid 438 and (name N or name CA \ or name C or name O or name CB )) or resid 439 through 455 or (resid 456 and (na \ me N or name CA or name C or name O or name CB )) or resid 457 through 469 or (r \ esid 470 through 471 and (name N or name CA or name C or name O or name CB )) or \ resid 472 through 473 or (resid 474 and (name N or name CA or name C or name O \ or name CB )) or resid 475 through 476 or (resid 477 and (name N or name CA or n \ ame C or name O or name CB )) or resid 478 through 485)) selection = (chain 'D' and (resid 15 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 34 or (resid 35 and (name N or nam \ e CA or name C or name O or name CB )) or resid 36 through 39 or (resid 40 and ( \ name N or name CA or name C or name O or name CB )) or resid 41 through 50 or (r \ esid 51 through 52 and (name N or name CA or name C or name O or name CB )) or r \ esid 53 through 70 or (resid 71 and (name N or name CA or name C or name O or na \ me CB )) or resid 72 through 83 or (resid 84 and (name N or name CA or name C or \ name O or name CB )) or resid 85 through 124 or (resid 125 and (name N or name \ CA or name C or name O or name CB )) or resid 126 through 132 or (resid 133 and \ (name N or name CA or name C or name O or name CB )) or resid 134 through 136 or \ (resid 137 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 8 through 151 or (resid 152 and (name N or name CA or name C or name O or name C \ B )) or resid 153 through 155 or (resid 156 through 157 and (name N or name CA o \ r name C or name O or name CB )) or resid 158 through 169 or (resid 170 and (nam \ e N or name CA or name C or name O or name CB )) or resid 171 through 220 or (re \ sid 221 through 222 and (name N or name CA or name C or name O or name CB )) or \ resid 223 through 229 or (resid 230 through 232 and (name N or name CA or name C \ or name O or name CB )) or resid 233 through 235 or (resid 236 and (name N or n \ ame CA or name C or name O or name CB )) or resid 237 through 245 or (resid 246 \ through 247 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 8 through 263 or (resid 264 and (name N or name CA or name C or name O or name C \ B )) or resid 265 through 316 or (resid 317 and (name N or name CA or name C or \ name O or name CB )) or resid 318 through 339 or (resid 340 through 341 and (nam \ e N or name CA or name C or name O or name CB )) or resid 342 or (resid 343 and \ (name N or name CA or name C or name O or name CB )) or resid 344 through 384 or \ (resid 385 through 387 and (name N or name CA or name C or name O or name CB )) \ or (resid 388 through 392 and (name N or name CA or name C or name O or name CB \ )) or resid 393 through 397 or (resid 398 and (name N or name CA or name C or n \ ame O or name CB )) or resid 399 through 415 or (resid 416 through 420 and (name \ N or name CA or name C or name O or name CB )) or (resid 421 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 437 or ( \ resid 438 and (name N or name CA or name C or name O or name CB )) or resid 439 \ through 440 or (resid 441 and (name N or name CA or name C or name O or name CB \ )) or resid 442 through 473 or (resid 474 and (name N or name CA or name C or na \ me O or name CB )) or resid 475 through 482 or (resid 483 and (name N or name CA \ or name C or name O or name CB )) or resid 484 through 485)) selection = (chain 'F' and ((resid 15 through 18 and (name N or name CA or name C or name O \ or name CB )) or resid 19 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 31 or (resid 32 and (name N or na \ me CA or name C or name O or name CB )) or resid 33 through 34 or (resid 35 and \ (name N or name CA or name C or name O or name CB )) or resid 36 through 39 or ( \ resid 40 and (name N or name CA or name C or name O or name CB )) or resid 41 th \ rough 50 or (resid 51 through 52 and (name N or name CA or name C or name O or n \ ame CB )) or resid 53 through 60 or (resid 61 and (name N or name CA or name C o \ r name O or name CB )) or resid 62 through 88 or (resid 89 through 90 and (name \ N or name CA or name C or name O or name CB )) or resid 91 through 98 or (resid \ 99 and (name N or name CA or name C or name O or name CB )) or resid 100 through \ 104 or (resid 105 through 107 and (name N or name CA or name C or name O or nam \ e CB )) or resid 108 through 120 or (resid 121 through 122 and (name N or name C \ A or name C or name O or name CB )) or resid 123 through 151 or (resid 152 and ( \ name N or name CA or name C or name O or name CB )) or resid 153 through 155 or \ (resid 156 through 157 and (name N or name CA or name C or name O or name CB )) \ or resid 158 through 169 or (resid 170 and (name N or name CA or name C or name \ O or name CB )) or resid 171 through 208 or (resid 209 and (name N or name CA or \ name C or name O or name CB )) or resid 210 through 217 or (resid 218 and (name \ N or name CA or name C or name O or name CB )) or resid 219 through 226 or (res \ id 227 and (name N or name CA or name C or name O or name CB )) or resid 228 thr \ ough 229 or (resid 230 through 232 and (name N or name CA or name C or name O or \ name CB )) or resid 233 or (resid 234 and (name N or name CA or name C or name \ O or name CB )) or resid 235 through 238 or (resid 239 and (name N or name CA or \ name C or name O or name CB )) or resid 240 through 245 or (resid 246 through 2 \ 47 and (name N or name CA or name C or name O or name CB )) or resid 248 through \ 263 or (resid 264 and (name N or name CA or name C or name O or name CB )) or r \ esid 265 through 270 or (resid 271 and (name N or name CA or name C or name O or \ name CB )) or resid 272 through 282 or (resid 283 and (name N or name CA or nam \ e C or name O or name CB )) or resid 284 through 285 or (resid 286 through 287 a \ nd (name N or name CA or name C or name O or name CB )) or resid 288 through 289 \ or (resid 290 and (name N or name CA or name C or name O or name CB )) or resid \ 291 through 295 or (resid 296 through 297 and (name N or name CA or name C or n \ ame O or name CB )) or resid 298 through 300 or (resid 301 and (name N or name C \ A or name C or name O or name CB )) or resid 302 through 312 or (resid 313 and ( \ name N or name CA or name C or name O or name CB )) or resid 314 through 325 or \ (resid 326 and (name N or name CA or name C or name O or name CB )) or resid 327 \ or (resid 328 and (name N or name CA or name C or name O or name CB )) or resid \ 329 through 338 or (resid 339 through 341 and (name N or name CA or name C or n \ ame O or name CB )) or resid 342 or (resid 343 and (name N or name CA or name C \ or name O or name CB )) or resid 344 through 347 or (resid 348 and (name N or na \ me CA or name C or name O or name CB )) or resid 349 through 379 or (resid 380 a \ nd (name N or name CA or name C or name O or name CB )) or resid 381 through 384 \ or (resid 385 through 387 and (name N or name CA or name C or name O or name CB \ )) or (resid 388 through 392 and (name N or name CA or name C or name O or name \ CB )) or resid 393 through 397 or (resid 398 and (name N or name CA or name C o \ r name O or name CB )) or resid 399 or (resid 400 through 401 and (name N or nam \ e CA or name C or name O or name CB )) or resid 402 through 440 or (resid 441 an \ d (name N or name CA or name C or name O or name CB )) or resid 442 through 462 \ or (resid 463 and (name N or name CA or name C or name O or name CB )) or resid \ 464 through 469 or (resid 470 through 471 and (name N or name CA or name C or na \ me O or name CB )) or resid 472 through 485)) } ncs_group { reference = (chain 'G' and ((resid 45 through 84 and (name N or name CA or name C or name O \ or name CB )) or resid 85 through 89 or (resid 90 through 91 and (name N or name \ CA or name C or name O or name CB )) or resid 92 through 93 or (resid 94 throug \ h 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 101 or (resid 102 through 106 and (name N or name CA or name C or name O or na \ me CB )) or resid 107 through 109 or (resid 110 through 116 and (name N or name \ CA or name C or name O or name CB )) or resid 117 through 122 or (resid 123 and \ (name N or name CA or name C or name O or name CB )) or resid 124 through 145 or \ (resid 146 through 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 157 or (resid 158 and (name N or name CA or name C or name \ O or name CB )) or resid 159 through 164 or (resid 165 through 167 and (name N \ or name CA or name C or name O or name CB )) or resid 168 through 174 or (resid \ 175 through 177 and (name N or name CA or name C or name O or name CB )) or resi \ d 178 through 183 or (resid 184 through 185 and (name N or name CA or name C or \ name O or name CB )) or resid 186 through 199 or (resid 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 227 or (resid 228 and \ (name N or name CA or name C or name O or name CB )) or resid 229 through 231)) selection = (chain 'I' and (resid 45 through 92 or (resid 93 through 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 101 or (resid 102 throu \ gh 106 and (name N or name CA or name C or name O or name CB )) or resid 107 thr \ ough 117 or (resid 118 and (name N or name CA or name C or name O or name CB )) \ or resid 119 through 122 or (resid 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 through 126 or (resid 127 through 128 and (name N o \ r name CA or name C or name O or name CB )) or resid 129 through 133 or (resid 1 \ 34 and (name N or name CA or name C or name O or name CB )) or resid 135 through \ 183 or (resid 184 through 185 and (name N or name CA or name C or name O or nam \ e CB )) or resid 186 through 197 or (resid 198 and (name N or name CA or name C \ or name O or name CB )) or resid 199 or (resid 200 and (name N or name CA or nam \ e C or name O or name CB )) or resid 201 through 204 or (resid 205 and (name N o \ r name CA or name C or name O or name CB )) or resid 206 through 210 or (resid 2 \ 11 through 214 and (name N or name CA or name C or name O or name CB )) or resid \ 215 through 226 or (resid 227 through 228 and (name N or name CA or name C or n \ ame O or name CB )) or resid 229 through 231)) selection = (chain 'K' and ((resid 45 through 84 and (name N or name CA or name C or name O \ or name CB )) or resid 85 through 92 or (resid 93 through 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 103 or (resid 104 thro \ ugh 106 and (name N or name CA or name C or name O or name CB )) or resid 107 th \ rough 109 or (resid 110 through 116 and (name N or name CA or name C or name O o \ r name CB )) or resid 117 or (resid 118 and (name N or name CA or name C or name \ O or name CB )) or resid 119 through 135 or (resid 136 through 137 and (name N \ or name CA or name C or name O or name CB )) or resid 138 through 145 or (resid \ 146 through 147 and (name N or name CA or name C or name O or name CB )) or resi \ d 148 through 164 or (resid 165 through 167 and (name N or name CA or name C or \ name O or name CB )) or resid 168 through 175 or (resid 176 through 177 and (nam \ e N or name CA or name C or name O or name CB )) or resid 178 through 231)) } ncs_group { reference = (chain 'H' and ((resid 29 through 77 and (name N or name CA or name C or name O \ or name CB )) or resid 78 or (resid 79 and (name N or name CA or name C or name \ O or name CB )) or resid 80 through 103 or (resid 104 and (name N or name CA or \ name C or name O or name CB )) or resid 105 or (resid 106 through 108 and (name \ N or name CA or name C or name O or name CB )) or resid 109 through 110 or (resi \ d 111 through 112 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'L' and (resid 29 through 83 or (resid 84 through 90 and (name N or name \ CA or name C or name O or name CB )) or resid 91 through 99 or (resid 100 and (n \ ame N or name CA or name C or name O or name CB )) or resid 101 through 112)) } 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: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.810 Check model and map are aligned: 0.440 Set scattering table: 0.300 Process input model: 87.530 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32641 Z= 0.252 Angle : 0.544 8.818 44701 Z= 0.298 Chirality : 0.042 0.306 5517 Planarity : 0.004 0.073 5807 Dihedral : 12.381 89.894 10426 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.45 % Rotamer: Outliers : 0.38 % Allowed : 0.42 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.23 (0.13), residues: 4765 helix: 2.24 (0.11), residues: 2415 sheet: -1.94 (0.22), residues: 522 loop : -0.22 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 462 HIS 0.005 0.001 HIS B 396 PHE 0.016 0.001 PHE A 438 TYR 0.021 0.001 TYR A 531 ARG 0.007 0.000 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 434 time to evaluate : 3.479 Fit side-chains REVERT: B 161 MET cc_start: 0.8237 (tpp) cc_final: 0.7962 (mmm) REVERT: C 193 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8220 (tp) REVERT: G 90 SER cc_start: 0.8732 (m) cc_final: 0.8350 (m) REVERT: M 61 MET cc_start: 0.8467 (ptt) cc_final: 0.7776 (ppp) outliers start: 9 outliers final: 2 residues processed: 441 average time/residue: 0.4526 time to fit residues: 316.3111 Evaluate side-chains 364 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 361 time to evaluate : 3.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 3.9990 chunk 358 optimal weight: 0.9990 chunk 198 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 370 optimal weight: 50.0000 chunk 143 optimal weight: 0.8980 chunk 225 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 429 optimal weight: 50.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN A 497 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN C 140 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN F 190 GLN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 32641 Z= 0.364 Angle : 0.550 8.440 44701 Z= 0.285 Chirality : 0.044 0.210 5517 Planarity : 0.005 0.054 5807 Dihedral : 4.736 75.725 5131 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.75 % Rotamer: Outliers : 1.09 % Allowed : 8.97 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.14 (0.12), residues: 4765 helix: 2.23 (0.11), residues: 2375 sheet: -2.24 (0.21), residues: 548 loop : -0.17 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 462 HIS 0.005 0.001 HIS B 396 PHE 0.020 0.001 PHE A 438 TYR 0.019 0.001 TYR B 49 ARG 0.005 0.001 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 389 time to evaluate : 3.661 Fit side-chains revert: symmetry clash REVERT: B 161 MET cc_start: 0.8407 (tpp) cc_final: 0.7978 (mmm) REVERT: C 352 MET cc_start: 0.8555 (ttt) cc_final: 0.8259 (ttt) REVERT: D 416 MET cc_start: 0.7174 (tpp) cc_final: 0.6863 (tpt) REVERT: E 294 LEU cc_start: 0.9030 (mt) cc_final: 0.8788 (mt) REVERT: E 359 ARG cc_start: 0.8332 (mmp80) cc_final: 0.7680 (mmt90) REVERT: G 90 SER cc_start: 0.8759 (m) cc_final: 0.8292 (m) REVERT: I 220 LEU cc_start: 0.8477 (tt) cc_final: 0.8246 (tp) REVERT: K 157 MET cc_start: 0.8334 (mtt) cc_final: 0.8053 (mtt) REVERT: M 61 MET cc_start: 0.8536 (ptt) cc_final: 0.7818 (ppp) outliers start: 26 outliers final: 21 residues processed: 403 average time/residue: 0.4944 time to fit residues: 314.8287 Evaluate side-chains 386 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 365 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 238 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 357 optimal weight: 1.9990 chunk 292 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 430 optimal weight: 9.9990 chunk 464 optimal weight: 20.0000 chunk 383 optimal weight: 0.9990 chunk 426 optimal weight: 40.0000 chunk 146 optimal weight: 1.9990 chunk 345 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN A 497 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN D 50 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 32641 Z= 0.373 Angle : 0.547 7.539 44701 Z= 0.281 Chirality : 0.044 0.304 5517 Planarity : 0.004 0.066 5807 Dihedral : 4.624 75.960 5128 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.21 % Favored : 96.77 % Rotamer: Outliers : 1.89 % Allowed : 11.44 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.04 (0.12), residues: 4765 helix: 2.19 (0.11), residues: 2369 sheet: -2.26 (0.21), residues: 540 loop : -0.28 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 541 HIS 0.005 0.001 HIS B 396 PHE 0.020 0.001 PHE A 438 TYR 0.016 0.001 TYR B 49 ARG 0.006 0.001 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 368 time to evaluate : 3.658 Fit side-chains REVERT: B 161 MET cc_start: 0.8554 (tpp) cc_final: 0.8021 (mmm) REVERT: B 384 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8255 (mtmt) REVERT: B 468 TYR cc_start: 0.8753 (m-80) cc_final: 0.8497 (m-80) REVERT: E 294 LEU cc_start: 0.9004 (mt) cc_final: 0.8700 (mt) REVERT: G 90 SER cc_start: 0.8697 (m) cc_final: 0.8245 (m) REVERT: I 149 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7931 (mt) REVERT: I 220 LEU cc_start: 0.8515 (tt) cc_final: 0.8239 (tp) REVERT: L 90 LYS cc_start: 0.7786 (mtpp) cc_final: 0.7297 (tttt) REVERT: M 61 MET cc_start: 0.8500 (ptt) cc_final: 0.7772 (ppp) outliers start: 45 outliers final: 29 residues processed: 391 average time/residue: 0.5732 time to fit residues: 357.1886 Evaluate side-chains 380 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 350 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 425 optimal weight: 40.0000 chunk 323 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 431 optimal weight: 6.9990 chunk 457 optimal weight: 40.0000 chunk 225 optimal weight: 0.4980 chunk 409 optimal weight: 30.0000 chunk 123 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 32641 Z= 0.498 Angle : 0.604 7.882 44701 Z= 0.311 Chirality : 0.046 0.197 5517 Planarity : 0.005 0.074 5807 Dihedral : 4.755 74.862 5128 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.74 % Favored : 96.24 % Rotamer: Outliers : 2.72 % Allowed : 13.66 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 0.78 (0.12), residues: 4765 helix: 1.96 (0.11), residues: 2379 sheet: -2.29 (0.20), residues: 556 loop : -0.41 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 541 HIS 0.006 0.002 HIS A 213 PHE 0.020 0.002 PHE B 439 TYR 0.017 0.002 TYR F 370 ARG 0.008 0.001 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 357 time to evaluate : 3.992 Fit side-chains REVERT: A 45 MET cc_start: 0.8709 (mmm) cc_final: 0.8433 (mmm) REVERT: A 234 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8824 (mm) REVERT: A 435 THR cc_start: 0.8902 (t) cc_final: 0.8645 (p) REVERT: B 161 MET cc_start: 0.8591 (tpp) cc_final: 0.7958 (mmm) REVERT: B 384 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8535 (mtmt) REVERT: C 294 LEU cc_start: 0.8424 (mp) cc_final: 0.8219 (mp) REVERT: C 320 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8311 (t0) REVERT: E 108 ILE cc_start: 0.8507 (mt) cc_final: 0.8203 (mt) REVERT: E 294 LEU cc_start: 0.9058 (mt) cc_final: 0.8769 (mt) REVERT: G 90 SER cc_start: 0.8721 (m) cc_final: 0.8291 (m) REVERT: I 87 LYS cc_start: 0.8061 (ttmm) cc_final: 0.7642 (ttmm) REVERT: L 90 LYS cc_start: 0.7836 (mtpp) cc_final: 0.7329 (tttt) REVERT: M 61 MET cc_start: 0.8515 (ptt) cc_final: 0.7803 (ppp) REVERT: M 197 ARG cc_start: 0.8345 (ttm110) cc_final: 0.8142 (ttm110) outliers start: 65 outliers final: 43 residues processed: 403 average time/residue: 0.4936 time to fit residues: 314.2812 Evaluate side-chains 388 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 343 time to evaluate : 4.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 380 optimal weight: 0.8980 chunk 259 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 340 optimal weight: 9.9990 chunk 188 optimal weight: 0.7980 chunk 390 optimal weight: 8.9990 chunk 316 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 233 optimal weight: 0.9980 chunk 410 optimal weight: 6.9990 chunk 115 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN F 190 GLN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32641 Z= 0.238 Angle : 0.496 8.970 44701 Z= 0.253 Chirality : 0.042 0.338 5517 Planarity : 0.004 0.051 5807 Dihedral : 4.420 76.093 5128 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.73 % Favored : 97.25 % Rotamer: Outliers : 1.97 % Allowed : 15.21 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.01 (0.13), residues: 4765 helix: 2.16 (0.11), residues: 2373 sheet: -2.25 (0.21), residues: 548 loop : -0.30 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 541 HIS 0.004 0.001 HIS B 396 PHE 0.016 0.001 PHE B 439 TYR 0.016 0.001 TYR A 531 ARG 0.007 0.000 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 372 time to evaluate : 3.427 Fit side-chains REVERT: A 234 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8812 (mm) REVERT: A 435 THR cc_start: 0.8842 (t) cc_final: 0.8567 (p) REVERT: B 161 MET cc_start: 0.8559 (tpp) cc_final: 0.7899 (mmm) REVERT: B 315 ILE cc_start: 0.9037 (mm) cc_final: 0.8776 (mm) REVERT: B 342 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.7615 (mp) REVERT: B 383 MET cc_start: 0.8062 (ttp) cc_final: 0.7719 (ttt) REVERT: B 384 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8334 (mtmt) REVERT: C 478 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.7326 (t80) REVERT: E 334 TYR cc_start: 0.8828 (m-80) cc_final: 0.8586 (m-80) REVERT: F 275 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8439 (tt) REVERT: F 442 THR cc_start: 0.8383 (m) cc_final: 0.8053 (p) REVERT: G 90 SER cc_start: 0.8724 (m) cc_final: 0.8344 (m) REVERT: I 87 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7708 (ttmm) REVERT: K 157 MET cc_start: 0.8258 (mtt) cc_final: 0.8008 (mtt) REVERT: M 61 MET cc_start: 0.8499 (ptt) cc_final: 0.7799 (ppp) outliers start: 47 outliers final: 29 residues processed: 404 average time/residue: 0.4777 time to fit residues: 305.8161 Evaluate side-chains 388 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 354 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 153 optimal weight: 0.0980 chunk 411 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 457 optimal weight: 30.0000 chunk 379 optimal weight: 1.9990 chunk 211 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 240 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32641 Z= 0.264 Angle : 0.502 7.648 44701 Z= 0.256 Chirality : 0.042 0.264 5517 Planarity : 0.004 0.050 5807 Dihedral : 4.340 76.382 5126 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 2.60 % Allowed : 15.71 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.06 (0.13), residues: 4765 helix: 2.24 (0.11), residues: 2365 sheet: -2.22 (0.20), residues: 576 loop : -0.29 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 541 HIS 0.006 0.001 HIS E 450 PHE 0.017 0.001 PHE B 439 TYR 0.013 0.001 TYR B 49 ARG 0.008 0.000 ARG M 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 364 time to evaluate : 3.622 Fit side-chains REVERT: A 234 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8822 (mm) REVERT: A 435 THR cc_start: 0.8878 (t) cc_final: 0.8586 (p) REVERT: B 161 MET cc_start: 0.8586 (tpp) cc_final: 0.7944 (mmm) REVERT: B 315 ILE cc_start: 0.9028 (mm) cc_final: 0.8778 (mm) REVERT: B 342 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.7612 (mp) REVERT: B 383 MET cc_start: 0.8035 (ttp) cc_final: 0.7728 (ttt) REVERT: B 384 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8404 (mtmt) REVERT: C 95 GLU cc_start: 0.7838 (tp30) cc_final: 0.7616 (tt0) REVERT: C 478 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.7261 (t80) REVERT: D 260 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8469 (mm) REVERT: E 294 LEU cc_start: 0.8987 (mt) cc_final: 0.8766 (mt) REVERT: E 334 TYR cc_start: 0.8852 (m-80) cc_final: 0.8601 (m-80) REVERT: F 275 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8448 (tt) REVERT: F 339 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8223 (m-40) REVERT: F 442 THR cc_start: 0.8394 (m) cc_final: 0.8057 (p) REVERT: G 90 SER cc_start: 0.8710 (m) cc_final: 0.8315 (m) REVERT: I 87 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7742 (ttmm) REVERT: K 157 MET cc_start: 0.8252 (mtt) cc_final: 0.8017 (mtt) REVERT: M 61 MET cc_start: 0.8512 (ptt) cc_final: 0.7821 (ppp) outliers start: 62 outliers final: 44 residues processed: 402 average time/residue: 0.4792 time to fit residues: 306.4365 Evaluate side-chains 406 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 355 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 441 optimal weight: 50.0000 chunk 51 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 chunk 334 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 chunk 385 optimal weight: 0.3980 chunk 255 optimal weight: 0.9990 chunk 455 optimal weight: 40.0000 chunk 285 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 32641 Z= 0.397 Angle : 0.554 8.415 44701 Z= 0.282 Chirality : 0.044 0.262 5517 Planarity : 0.004 0.058 5807 Dihedral : 4.460 75.835 5126 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 3.39 % Allowed : 15.75 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 0.93 (0.13), residues: 4765 helix: 2.11 (0.11), residues: 2372 sheet: -2.27 (0.21), residues: 547 loop : -0.37 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 541 HIS 0.005 0.001 HIS A 213 PHE 0.018 0.001 PHE B 439 TYR 0.014 0.001 TYR F 370 ARG 0.007 0.001 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 355 time to evaluate : 3.650 Fit side-chains REVERT: A 234 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8833 (mm) REVERT: A 435 THR cc_start: 0.8935 (t) cc_final: 0.8652 (p) REVERT: B 161 MET cc_start: 0.8653 (tpp) cc_final: 0.7978 (mmm) REVERT: B 315 ILE cc_start: 0.9053 (mm) cc_final: 0.8821 (mm) REVERT: B 342 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.7710 (mp) REVERT: C 95 GLU cc_start: 0.7876 (tp30) cc_final: 0.7672 (tt0) REVERT: C 478 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.7186 (t80) REVERT: E 294 LEU cc_start: 0.8981 (mt) cc_final: 0.8681 (mt) REVERT: E 334 TYR cc_start: 0.8896 (m-80) cc_final: 0.8599 (m-80) REVERT: E 352 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.7855 (tmt) REVERT: F 275 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8489 (tt) REVERT: F 339 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8281 (m110) REVERT: G 90 SER cc_start: 0.8752 (m) cc_final: 0.8355 (m) REVERT: I 87 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7743 (ttmm) REVERT: M 61 MET cc_start: 0.8526 (ptt) cc_final: 0.7826 (ppp) outliers start: 81 outliers final: 59 residues processed: 410 average time/residue: 0.4725 time to fit residues: 307.6678 Evaluate side-chains 405 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 340 time to evaluate : 3.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 352 MET Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 607 MET Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 163 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 282 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 272 optimal weight: 0.0970 chunk 137 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 289 optimal weight: 0.9990 chunk 310 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 358 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32641 Z= 0.194 Angle : 0.484 8.572 44701 Z= 0.246 Chirality : 0.041 0.204 5517 Planarity : 0.004 0.051 5807 Dihedral : 4.265 76.365 5126 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.69 % Favored : 97.29 % Rotamer: Outliers : 1.97 % Allowed : 17.09 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.13 (0.13), residues: 4765 helix: 2.28 (0.11), residues: 2372 sheet: -2.24 (0.20), residues: 585 loop : -0.21 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 541 HIS 0.003 0.001 HIS E 450 PHE 0.014 0.001 PHE D 439 TYR 0.020 0.001 TYR A 531 ARG 0.006 0.000 ARG M 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 365 time to evaluate : 3.583 Fit side-chains REVERT: A 234 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8803 (mm) REVERT: A 435 THR cc_start: 0.8850 (t) cc_final: 0.8543 (p) REVERT: A 610 ARG cc_start: 0.7648 (mmm-85) cc_final: 0.6960 (tpt90) REVERT: B 161 MET cc_start: 0.8541 (tpp) cc_final: 0.7948 (mmm) REVERT: B 315 ILE cc_start: 0.9012 (mm) cc_final: 0.8741 (mm) REVERT: B 342 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7574 (mp) REVERT: B 384 LYS cc_start: 0.8532 (mtmt) cc_final: 0.8297 (mtmt) REVERT: C 95 GLU cc_start: 0.7821 (tp30) cc_final: 0.7526 (tt0) REVERT: E 334 TYR cc_start: 0.8830 (m-80) cc_final: 0.8596 (m-80) REVERT: F 275 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8455 (tt) REVERT: F 442 THR cc_start: 0.8407 (m) cc_final: 0.8074 (p) REVERT: G 90 SER cc_start: 0.8708 (m) cc_final: 0.8327 (m) REVERT: I 87 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7828 (ttmm) REVERT: I 127 GLU cc_start: 0.8225 (tt0) cc_final: 0.7781 (tt0) REVERT: K 176 ASN cc_start: 0.7817 (t0) cc_final: 0.7617 (m-40) REVERT: M 61 MET cc_start: 0.8527 (ptt) cc_final: 0.7819 (ppp) outliers start: 47 outliers final: 35 residues processed: 395 average time/residue: 0.4698 time to fit residues: 293.9804 Evaluate side-chains 396 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 358 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 414 optimal weight: 2.9990 chunk 436 optimal weight: 20.0000 chunk 398 optimal weight: 0.7980 chunk 424 optimal weight: 50.0000 chunk 255 optimal weight: 0.6980 chunk 185 optimal weight: 0.0770 chunk 333 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 383 optimal weight: 0.9990 chunk 401 optimal weight: 1.9990 chunk 423 optimal weight: 30.0000 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32641 Z= 0.272 Angle : 0.512 11.633 44701 Z= 0.259 Chirality : 0.042 0.265 5517 Planarity : 0.004 0.052 5807 Dihedral : 4.277 76.105 5126 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.25 % Favored : 96.73 % Rotamer: Outliers : 2.14 % Allowed : 16.97 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.11 (0.13), residues: 4765 helix: 2.26 (0.11), residues: 2374 sheet: -2.23 (0.20), residues: 587 loop : -0.21 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 541 HIS 0.004 0.001 HIS B 396 PHE 0.015 0.001 PHE B 439 TYR 0.014 0.001 TYR A 531 ARG 0.008 0.000 ARG M 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 360 time to evaluate : 3.731 Fit side-chains REVERT: A 234 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8780 (mm) REVERT: A 435 THR cc_start: 0.8882 (t) cc_final: 0.8581 (p) REVERT: A 610 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.6967 (tpt90) REVERT: B 161 MET cc_start: 0.8621 (tpp) cc_final: 0.8013 (mmm) REVERT: B 315 ILE cc_start: 0.9017 (mm) cc_final: 0.8770 (mm) REVERT: B 342 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.7575 (mp) REVERT: B 384 LYS cc_start: 0.8513 (mtmt) cc_final: 0.8282 (mtmt) REVERT: C 95 GLU cc_start: 0.7850 (tp30) cc_final: 0.7542 (tt0) REVERT: C 478 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.7215 (t80) REVERT: E 334 TYR cc_start: 0.8867 (m-80) cc_final: 0.8645 (m-80) REVERT: F 275 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8458 (tt) REVERT: F 442 THR cc_start: 0.8415 (m) cc_final: 0.8073 (p) REVERT: G 90 SER cc_start: 0.8715 (m) cc_final: 0.8340 (m) REVERT: I 87 LYS cc_start: 0.8104 (ttmm) cc_final: 0.7881 (ttmm) REVERT: I 118 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8259 (tttm) REVERT: I 127 GLU cc_start: 0.8232 (tt0) cc_final: 0.7806 (tt0) REVERT: L 84 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8198 (mttp) REVERT: M 61 MET cc_start: 0.8536 (ptt) cc_final: 0.7834 (ppp) outliers start: 51 outliers final: 41 residues processed: 394 average time/residue: 0.4912 time to fit residues: 310.5645 Evaluate side-chains 399 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 353 time to evaluate : 3.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 163 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 278 optimal weight: 0.7980 chunk 449 optimal weight: 7.9990 chunk 274 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 312 optimal weight: 0.8980 chunk 471 optimal weight: 50.0000 chunk 433 optimal weight: 9.9990 chunk 375 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 289 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 32641 Z= 0.313 Angle : 0.533 12.131 44701 Z= 0.269 Chirality : 0.043 0.277 5517 Planarity : 0.004 0.055 5807 Dihedral : 4.334 75.588 5126 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.25 % Favored : 96.73 % Rotamer: Outliers : 2.26 % Allowed : 16.72 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.06 (0.13), residues: 4765 helix: 2.23 (0.11), residues: 2369 sheet: -2.12 (0.20), residues: 586 loop : -0.30 (0.15), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 541 HIS 0.004 0.001 HIS A 213 PHE 0.016 0.001 PHE B 439 TYR 0.013 0.001 TYR A 531 ARG 0.007 0.000 ARG A 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 355 time to evaluate : 3.748 Fit side-chains REVERT: A 234 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8777 (mm) REVERT: A 435 THR cc_start: 0.8898 (t) cc_final: 0.8613 (p) REVERT: A 610 ARG cc_start: 0.7671 (mmm-85) cc_final: 0.6976 (tpt90) REVERT: B 161 MET cc_start: 0.8693 (tpp) cc_final: 0.8066 (mmm) REVERT: B 315 ILE cc_start: 0.9026 (mm) cc_final: 0.8794 (mm) REVERT: B 342 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7592 (mp) REVERT: C 95 GLU cc_start: 0.7865 (tp30) cc_final: 0.7566 (tt0) REVERT: C 478 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.7203 (t80) REVERT: E 334 TYR cc_start: 0.8877 (m-80) cc_final: 0.8611 (m-80) REVERT: E 352 MET cc_start: 0.8429 (tmm) cc_final: 0.8222 (ttt) REVERT: F 275 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8486 (tt) REVERT: F 442 THR cc_start: 0.8454 (m) cc_final: 0.8109 (p) REVERT: G 90 SER cc_start: 0.8715 (m) cc_final: 0.8321 (m) REVERT: I 87 LYS cc_start: 0.8107 (ttmm) cc_final: 0.7836 (ttmm) REVERT: I 118 LYS cc_start: 0.8595 (ttmt) cc_final: 0.8257 (tttm) REVERT: I 127 GLU cc_start: 0.8299 (tt0) cc_final: 0.7901 (tt0) REVERT: L 84 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8175 (mttp) REVERT: M 61 MET cc_start: 0.8545 (ptt) cc_final: 0.7835 (ppp) outliers start: 54 outliers final: 46 residues processed: 394 average time/residue: 0.5059 time to fit residues: 315.9758 Evaluate side-chains 402 residues out of total 4135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 351 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 163 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 298 optimal weight: 0.6980 chunk 399 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 345 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 104 optimal weight: 0.0370 chunk 375 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 385 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 ASN C 320 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.163403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.127244 restraints weight = 38524.376| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.87 r_work: 0.3210 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32641 Z= 0.267 Angle : 0.516 12.357 44701 Z= 0.260 Chirality : 0.042 0.270 5517 Planarity : 0.004 0.052 5807 Dihedral : 4.289 75.288 5126 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.15 % Favored : 96.83 % Rotamer: Outliers : 2.43 % Allowed : 16.72 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % 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: 1.11 (0.13), residues: 4765 helix: 2.26 (0.11), residues: 2376 sheet: -2.19 (0.20), residues: 587 loop : -0.23 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 541 HIS 0.004 0.001 HIS A 213 PHE 0.015 0.001 PHE B 439 TYR 0.023 0.001 TYR A 531 ARG 0.007 0.000 ARG A 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7311.93 seconds wall clock time: 133 minutes 47.17 seconds (8027.17 seconds total)