Starting phenix.real_space_refine on Sun Mar 24 09:25:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fde_31541/03_2024/7fde_31541.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fde_31541/03_2024/7fde_31541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fde_31541/03_2024/7fde_31541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fde_31541/03_2024/7fde_31541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fde_31541/03_2024/7fde_31541.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fde_31541/03_2024/7fde_31541.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.129 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1210 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 25046 2.51 5 N 6704 2.21 5 O 7681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 40": "OD1" <-> "OD2" Residue "G TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 228": "OD1" <-> "OD2" Residue "P TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39557 Number of models: 1 Model: "" Number of chains: 16 Chain: "O" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2878 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 347} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1833 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 876 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "A" Number of atoms: 4587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4587 Classifications: {'peptide': 594} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 563} Chain: "B" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3706 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain breaks: 1 Chain: "C" Number of atoms: 4587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4587 Classifications: {'peptide': 594} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 563} Chain: "D" Number of atoms: 3681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3681 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 442} Chain breaks: 1 Chain: "E" Number of atoms: 4587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4587 Classifications: {'peptide': 594} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 563} Chain: "F" Number of atoms: 3699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3699 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "K" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1613 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "L" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "M" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 3, 'TRANS': 214} Chain: "N" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 928 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "I" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1801 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 876 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "P" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1418 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 19.12, per 1000 atoms: 0.48 Number of scatterers: 39557 At special positions: 0 Unit cell: (147.96, 154.44, 189, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 7681 8.00 N 6704 7.00 C 25046 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: 15.03 Conformation dependent library (CDL) restraints added in 6.6 seconds 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9416 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 54 sheets defined 50.4% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'O' and resid 29 through 36 Processing helix chain 'O' and resid 60 through 89 Processing helix chain 'O' and resid 101 through 105 Processing helix chain 'O' and resid 106 through 113 removed outlier: 3.570A pdb=" N GLU O 112 " --> pdb=" O PRO O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 167 Processing helix chain 'O' and resid 180 through 184 Processing helix chain 'O' and resid 202 through 208 Processing helix chain 'O' and resid 210 through 214 removed outlier: 3.736A pdb=" N LEU O 213 " --> pdb=" O TYR O 210 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER O 214 " --> pdb=" O GLU O 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 210 through 214' Processing helix chain 'O' and resid 241 through 253 removed outlier: 4.088A pdb=" N GLU O 245 " --> pdb=" O LYS O 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 265 through 319 removed outlier: 3.517A pdb=" N GLN O 269 " --> pdb=" O GLU O 265 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN O 282 " --> pdb=" O ALA O 278 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG O 285 " --> pdb=" O GLU O 281 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE O 300 " --> pdb=" O TYR O 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 336 through 349 Processing helix chain 'O' and resid 350 through 353 Processing helix chain 'G' and resid 11 through 111 removed outlier: 3.849A pdb=" N LYS G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU G 102 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR G 103 " --> pdb=" O ILE G 99 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS G 104 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU G 105 " --> pdb=" O GLU G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 133 Proline residue: G 119 - end of helix Processing helix chain 'G' and resid 145 through 164 removed outlier: 4.142A pdb=" N ASP G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASP G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 211 Processing helix chain 'G' and resid 214 through 223 Processing helix chain 'H' and resid 3 through 5 No H-bonds generated for 'chain 'H' and resid 3 through 5' Processing helix chain 'H' and resid 6 through 63 removed outlier: 3.883A pdb=" N LEU H 10 " --> pdb=" O GLY H 6 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN H 61 " --> pdb=" O PHE H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 76 removed outlier: 4.158A pdb=" N GLU H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 90 removed outlier: 3.521A pdb=" N LYS H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 104 Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.519A pdb=" N ILE A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 244 removed outlier: 4.015A pdb=" N ASP A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 331 through 346 removed outlier: 3.566A pdb=" N GLN A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 383 through 394 Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 443 through 449 removed outlier: 3.759A pdb=" N GLN A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 475 removed outlier: 4.547A pdb=" N LYS A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 503 removed outlier: 3.607A pdb=" N GLN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 507 Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'A' and resid 539 through 563 removed outlier: 3.510A pdb=" N THR A 543 " --> pdb=" O PRO A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 574 through 585 removed outlier: 4.064A pdb=" N LYS A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 616 Processing helix chain 'B' and resid 10 through 20 removed outlier: 3.731A pdb=" N LYS B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.551A pdb=" N MET B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 109' Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 155 through 163 removed outlier: 4.120A pdb=" N MET B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.732A pdb=" N GLU B 236 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 271 Proline residue: B 256 - end of helix Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 305 through 306 No H-bonds generated for 'chain 'B' and resid 305 through 306' Processing helix chain 'B' and resid 307 through 317 removed outlier: 3.795A pdb=" N ASP B 311 " --> pdb=" O TYR B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 361 through 367 removed outlier: 3.611A pdb=" N HIS B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 386 Processing helix chain 'B' and resid 395 through 420 removed outlier: 3.551A pdb=" N ASN B 401 " --> pdb=" O GLY B 397 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 443 Processing helix chain 'B' and resid 453 through 466 Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'C' and resid 111 through 120 removed outlier: 3.753A pdb=" N ILE C 115 " --> pdb=" O PRO C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 244 Processing helix chain 'C' and resid 261 through 273 removed outlier: 3.843A pdb=" N SER C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N GLN C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 297 removed outlier: 3.735A pdb=" N ALA C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'C' and resid 325 through 346 removed outlier: 3.885A pdb=" N ALA C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TYR C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C 346 " --> pdb=" O TYR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 372 Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 425 through 435 removed outlier: 3.571A pdb=" N THR C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 434 " --> pdb=" O ALA C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 463 through 475 removed outlier: 3.755A pdb=" N ASN C 468 " --> pdb=" O THR C 464 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 474 " --> pdb=" O PHE C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 503 removed outlier: 3.743A pdb=" N VAL C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 500 " --> pdb=" O GLU C 496 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU C 501 " --> pdb=" O GLN C 497 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 502 " --> pdb=" O VAL C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 525 Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.507A pdb=" N ALA C 536 " --> pdb=" O THR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 563 Processing helix chain 'C' and resid 566 through 584 removed outlier: 3.673A pdb=" N ASP C 572 " --> pdb=" O SER C 568 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASP C 576 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL C 577 " --> pdb=" O SER C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 587 No H-bonds generated for 'chain 'C' and resid 585 through 587' Processing helix chain 'C' and resid 594 through 616 Processing helix chain 'D' and resid 10 through 17 Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 105 through 109 removed outlier: 4.189A pdb=" N LEU D 109 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 179 through 191 Processing helix chain 'D' and resid 218 through 233 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 250 through 253 Processing helix chain 'D' and resid 254 through 270 Processing helix chain 'D' and resid 280 through 291 removed outlier: 3.738A pdb=" N TYR D 284 " --> pdb=" O ASP D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 306 No H-bonds generated for 'chain 'D' and resid 305 through 306' Processing helix chain 'D' and resid 307 through 318 removed outlier: 4.430A pdb=" N ARG D 318 " --> pdb=" O THR D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 354 Processing helix chain 'D' and resid 361 through 367 removed outlier: 3.770A pdb=" N HIS D 365 " --> pdb=" O ASP D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 387 Processing helix chain 'D' and resid 395 through 418 removed outlier: 3.786A pdb=" N SER D 400 " --> pdb=" O HIS D 396 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASN D 401 " --> pdb=" O GLY D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 443 removed outlier: 3.504A pdb=" N GLU D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 466 Processing helix chain 'D' and resid 477 through 486 removed outlier: 3.920A pdb=" N ASP D 486 " --> pdb=" O ASP D 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.834A pdb=" N ILE E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 244 Processing helix chain 'E' and resid 262 through 273 Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.694A pdb=" N ALA E 291 " --> pdb=" O GLY E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 346 removed outlier: 3.821A pdb=" N ALA E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN E 346 " --> pdb=" O TYR E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 372 removed outlier: 4.252A pdb=" N TRP E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 380 Processing helix chain 'E' and resid 383 through 394 removed outlier: 3.783A pdb=" N ARG E 394 " --> pdb=" O SER E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 433 Processing helix chain 'E' and resid 443 through 448 Processing helix chain 'E' and resid 467 through 475 removed outlier: 3.885A pdb=" N SER E 473 " --> pdb=" O LYS E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 503 removed outlier: 4.308A pdb=" N GLN E 497 " --> pdb=" O GLU E 493 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 507 Processing helix chain 'E' and resid 508 through 525 Processing helix chain 'E' and resid 539 through 565 removed outlier: 3.959A pdb=" N ALA E 565 " --> pdb=" O VAL E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 575 removed outlier: 4.022A pdb=" N ASP E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER E 573 " --> pdb=" O LYS E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 584 removed outlier: 3.536A pdb=" N HIS E 579 " --> pdb=" O GLY E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 587 No H-bonds generated for 'chain 'E' and resid 585 through 587' Processing helix chain 'E' and resid 594 through 614 Processing helix chain 'F' and resid 10 through 15 removed outlier: 3.536A pdb=" N ALA F 15 " --> pdb=" O ILE F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 20 removed outlier: 3.924A pdb=" N PHE F 20 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.758A pdb=" N LEU F 109 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 155 through 162 removed outlier: 3.902A pdb=" N MET F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'F' and resid 218 through 232 removed outlier: 3.539A pdb=" N ASN F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 249 through 253 Processing helix chain 'F' and resid 254 through 270 Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.523A pdb=" N TYR F 284 " --> pdb=" O ASP F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 317 Processing helix chain 'F' and resid 344 through 354 Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 382 through 387 Processing helix chain 'F' and resid 395 through 421 Processing helix chain 'F' and resid 426 through 443 Processing helix chain 'F' and resid 453 through 466 removed outlier: 3.600A pdb=" N SER F 463 " --> pdb=" O ASP F 459 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU F 465 " --> pdb=" O ALA F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 485 Processing helix chain 'K' and resid 32 through 50 Processing helix chain 'K' and resid 51 through 111 removed outlier: 3.734A pdb=" N LYS K 63 " --> pdb=" O ASP K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 133 Proline residue: K 119 - end of helix removed outlier: 3.810A pdb=" N LYS K 131 " --> pdb=" O GLU K 127 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU K 132 " --> pdb=" O ALA K 128 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU K 133 " --> pdb=" O LEU K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 152 removed outlier: 3.619A pdb=" N MET K 152 " --> pdb=" O LEU K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 164 Processing helix chain 'K' and resid 203 through 214 Processing helix chain 'K' and resid 214 through 223 Processing helix chain 'L' and resid 22 through 64 removed outlier: 3.556A pdb=" N LYS L 36 " --> pdb=" O LEU L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 75 removed outlier: 3.586A pdb=" N LYS L 70 " --> pdb=" O GLY L 66 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY L 75 " --> pdb=" O LYS L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 90 Processing helix chain 'L' and resid 90 through 103 removed outlier: 4.177A pdb=" N VAL L 94 " --> pdb=" O LYS L 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 75 removed outlier: 3.848A pdb=" N ASP M 45 " --> pdb=" O LYS M 41 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG M 59 " --> pdb=" O GLN M 55 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN M 62 " --> pdb=" O GLY M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 86 Processing helix chain 'M' and resid 126 through 140 removed outlier: 3.867A pdb=" N GLN M 130 " --> pdb=" O GLY M 126 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN M 131 " --> pdb=" O ARG M 127 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN M 133 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU M 137 " --> pdb=" O GLN M 133 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE M 138 " --> pdb=" O ARG M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 221 removed outlier: 4.031A pdb=" N THR M 145 " --> pdb=" O ARG M 141 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE M 178 " --> pdb=" O GLU M 174 " (cutoff:3.500A) Proline residue: M 179 - end of helix removed outlier: 3.879A pdb=" N ASP M 196 " --> pdb=" O LEU M 192 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG M 197 " --> pdb=" O ASP M 193 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU M 198 " --> pdb=" O GLU M 194 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU M 220 " --> pdb=" O LYS M 216 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET M 221 " --> pdb=" O LEU M 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 24 Processing helix chain 'N' and resid 46 through 59 Processing helix chain 'N' and resid 71 through 77 removed outlier: 3.618A pdb=" N ASN N 76 " --> pdb=" O HIS N 72 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE N 77 " --> pdb=" O ILE N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 84 removed outlier: 3.554A pdb=" N PHE N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 114 Processing helix chain 'I' and resid 8 through 87 removed outlier: 4.038A pdb=" N GLN I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN I 57 " --> pdb=" O ASN I 53 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET I 70 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN I 73 " --> pdb=" O ALA I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 113 removed outlier: 3.603A pdb=" N ASN I 112 " --> pdb=" O SER I 108 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 133 removed outlier: 3.869A pdb=" N ILE I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 144 No H-bonds generated for 'chain 'I' and resid 142 through 144' Processing helix chain 'I' and resid 145 through 152 removed outlier: 3.684A pdb=" N MET I 152 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 164 Processing helix chain 'I' and resid 202 through 214 removed outlier: 4.429A pdb=" N GLU I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU I 213 " --> pdb=" O LEU I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 224 Processing helix chain 'J' and resid 3 through 61 removed outlier: 4.283A pdb=" N ASP J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER J 45 " --> pdb=" O LYS J 41 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU J 53 " --> pdb=" O GLN J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 65 removed outlier: 3.694A pdb=" N VAL J 65 " --> pdb=" O ALA J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 62 through 65' Processing helix chain 'J' and resid 66 through 104 removed outlier: 3.957A pdb=" N ALA J 81 " --> pdb=" O GLN J 77 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL J 94 " --> pdb=" O LYS J 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 85 Processing helix chain 'P' and resid 110 through 118 Processing sheet with id=AA1, first strand: chain 'O' and resid 45 through 47 Processing sheet with id=AA2, first strand: chain 'O' and resid 223 through 227 removed outlier: 3.810A pdb=" N SER O 223 " --> pdb=" O ASN O 235 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU O 233 " --> pdb=" O ILE O 225 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU O 227 " --> pdb=" O TYR O 231 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR O 231 " --> pdb=" O GLU O 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE O 256 " --> pdb=" O ALA O 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 173 through 174 removed outlier: 3.675A pdb=" N VAL G 189 " --> pdb=" O LYS G 140 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL G 188 " --> pdb=" O ASN G 201 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL G 190 " --> pdb=" O ILE G 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA5, first strand: chain 'A' and resid 29 through 31 removed outlier: 4.050A pdb=" N ARG A 62 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLN A 71 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL A 60 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 93 through 96 Processing sheet with id=AA7, first strand: chain 'A' and resid 104 through 105 removed outlier: 6.749A pdb=" N ILE A 278 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL A 318 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR A 280 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 152 removed outlier: 6.683A pdb=" N GLU A 199 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 225 through 227 removed outlier: 4.106A pdb=" N GLU A 225 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS A 397 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 396 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 398 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 232 through 233 removed outlier: 4.364A pdb=" N CYS A 246 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 26 through 28 removed outlier: 5.779A pdb=" N ILE I 197 " --> pdb=" O ASN I 192 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL I 188 " --> pdb=" O ASN I 201 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA I 137 " --> pdb=" O GLU I 171 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.887A pdb=" N ALA B 75 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 78 " --> pdb=" O GLN B 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AB6, first strand: chain 'B' and resid 101 through 104 Processing sheet with id=AB7, first strand: chain 'B' and resid 112 through 113 removed outlier: 8.471A pdb=" N PHE B 241 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N PHE B 212 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N ILE B 332 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR B 276 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 150 through 151 removed outlier: 4.388A pdb=" N ILE B 164 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 25 through 31 removed outlier: 5.839A pdb=" N ILE C 27 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLU C 38 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 37 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LYS C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE C 63 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR C 69 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 86 " --> pdb=" O LYS C 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.664A pdb=" N VAL C 94 " --> pdb=" O TRP C 215 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP C 215 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 170 through 173 removed outlier: 4.471A pdb=" N GLY C 159 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 151 through 152 removed outlier: 6.594A pdb=" N GLU C 199 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 225 through 226 removed outlier: 3.808A pdb=" N GLU C 225 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 232 through 233 removed outlier: 4.643A pdb=" N CYS C 246 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 278 through 285 removed outlier: 3.585A pdb=" N THR C 316 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR C 280 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY C 284 " --> pdb=" O ASN C 320 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 302 through 303 Processing sheet with id=AC8, first strand: chain 'C' and resid 349 through 350 Processing sheet with id=AC9, first strand: chain 'D' and resid 27 through 28 Processing sheet with id=AD1, first strand: chain 'D' and resid 31 through 35 removed outlier: 5.635A pdb=" N ILE D 40 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL D 34 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU D 38 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA D 75 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE D 76 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 101 through 104 removed outlier: 3.516A pdb=" N ASP D 130 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 111 through 113 removed outlier: 6.839A pdb=" N ARG D 111 " --> pdb=" O LEU D 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.036A pdb=" N ARG D 321 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=AD6, first strand: chain 'D' and resid 209 through 214 removed outlier: 6.419A pdb=" N SER D 209 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE D 277 " --> pdb=" O SER D 209 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL D 211 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N THR D 279 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA D 213 " --> pdb=" O THR D 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 359 through 360 removed outlier: 4.424A pdb=" N PHE D 359 " --> pdb=" O ASN D 374 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 48 through 51 removed outlier: 3.788A pdb=" N VAL E 49 " --> pdb=" O GLY E 58 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL E 60 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN E 71 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG E 62 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 68 " --> pdb=" O ALA E 37 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E 37 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLU E 38 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE E 27 " --> pdb=" O GLU E 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 93 through 95 Processing sheet with id=AE1, first strand: chain 'E' and resid 104 through 105 Processing sheet with id=AE2, first strand: chain 'E' and resid 159 through 161 Processing sheet with id=AE3, first strand: chain 'E' and resid 151 through 152 removed outlier: 6.955A pdb=" N GLU E 199 " --> pdb=" O THR E 183 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 225 through 226 removed outlier: 4.023A pdb=" N GLU E 225 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 301 through 302 removed outlier: 3.541A pdb=" N GLU E 309 " --> pdb=" O THR E 302 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 34 through 35 removed outlier: 3.632A pdb=" N ARG F 74 " --> pdb=" O ARG F 71 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU F 69 " --> pdb=" O ILE F 76 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN F 78 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL F 67 " --> pdb=" O GLN F 78 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 101 through 104 removed outlier: 3.721A pdb=" N ASP F 130 " --> pdb=" O VAL F 104 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 112 through 113 removed outlier: 7.513A pdb=" N ALA F 213 " --> pdb=" O THR F 279 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 144 through 145 removed outlier: 3.791A pdb=" N ARG F 321 " --> pdb=" O ILE F 145 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 150 through 151 removed outlier: 4.616A pdb=" N ILE F 164 " --> pdb=" O ILE F 151 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 208 through 210 removed outlier: 6.202A pdb=" N SER F 209 " --> pdb=" O LEU F 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'K' and resid 171 through 174 removed outlier: 3.507A pdb=" N VAL K 189 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL K 188 " --> pdb=" O ASN K 201 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 95 through 96 removed outlier: 4.093A pdb=" N ARG M 95 " --> pdb=" O GLU M 110 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 99 through 100 Processing sheet with id=AF6, first strand: chain 'N' and resid 38 through 39 removed outlier: 7.524A pdb=" N PHE N 38 " --> pdb=" O ILE N 8 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL N 10 " --> pdb=" O PHE N 38 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU N 7 " --> pdb=" O ALA N 65 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU N 67 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA N 9 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE N 69 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE N 11 " --> pdb=" O ILE N 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU N 92 " --> pdb=" O LEU N 67 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 28 through 29 Processing sheet with id=AF8, first strand: chain 'P' and resid 99 through 103 removed outlier: 5.813A pdb=" N LEU P 100 " --> pdb=" O ARG P 271 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG P 271 " --> pdb=" O LEU P 100 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR P 102 " --> pdb=" O VAL P 269 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA P 266 " --> pdb=" O LYS P 135 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE P 165 " --> pdb=" O TYR P 145 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU P 166 " --> pdb=" O TYR P 205 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 241 through 243 1992 hydrogen bonds defined for protein. 5751 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: 16.35 Time building geometry restraints manager: 16.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13118 1.34 - 1.46: 5997 1.46 - 1.58: 20907 1.58 - 1.69: 0 1.69 - 1.81: 225 Bond restraints: 40247 Sorted by residual: bond pdb=" CG MET A 547 " pdb=" SD MET A 547 " ideal model delta sigma weight residual 1.803 1.760 0.043 2.50e-02 1.60e+03 2.91e+00 bond pdb=" CG GLU G 46 " pdb=" CD GLU G 46 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.59e+00 bond pdb=" CA VAL B 34 " pdb=" CB VAL B 34 " ideal model delta sigma weight residual 1.550 1.539 0.012 1.03e-02 9.43e+03 1.30e+00 bond pdb=" C ILE D 467 " pdb=" N TYR D 468 " ideal model delta sigma weight residual 1.331 1.299 0.032 2.83e-02 1.25e+03 1.29e+00 bond pdb=" CG LYS O 165 " pdb=" CD LYS O 165 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.22e+00 ... (remaining 40242 not shown) Histogram of bond angle deviations from ideal: 97.54 - 104.83: 653 104.83 - 112.12: 19942 112.12 - 119.41: 13758 119.41 - 126.70: 19632 126.70 - 133.98: 388 Bond angle restraints: 54373 Sorted by residual: angle pdb=" N GLU B 206 " pdb=" CA GLU B 206 " pdb=" CB GLU B 206 " ideal model delta sigma weight residual 114.17 109.95 4.22 1.14e+00 7.69e-01 1.37e+01 angle pdb=" C ILE G 45 " pdb=" N GLU G 46 " pdb=" CA GLU G 46 " ideal model delta sigma weight residual 120.68 114.64 6.04 1.70e+00 3.46e-01 1.26e+01 angle pdb=" N VAL F 375 " pdb=" CA VAL F 375 " pdb=" C VAL F 375 " ideal model delta sigma weight residual 113.71 110.57 3.14 9.50e-01 1.11e+00 1.09e+01 angle pdb=" C MET A 546 " pdb=" N MET A 547 " pdb=" CA MET A 547 " ideal model delta sigma weight residual 120.31 115.37 4.94 1.52e+00 4.33e-01 1.05e+01 angle pdb=" N GLU G 46 " pdb=" CA GLU G 46 " pdb=" CB GLU G 46 " ideal model delta sigma weight residual 110.30 115.04 -4.74 1.54e+00 4.22e-01 9.47e+00 ... (remaining 54368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 22602 17.81 - 35.62: 1777 35.62 - 53.43: 236 53.43 - 71.24: 36 71.24 - 89.05: 13 Dihedral angle restraints: 24664 sinusoidal: 10040 harmonic: 14624 Sorted by residual: dihedral pdb=" CA VAL F 291 " pdb=" C VAL F 291 " pdb=" N SER F 292 " pdb=" CA SER F 292 " ideal model delta harmonic sigma weight residual 180.00 150.38 29.62 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA HIS E 450 " pdb=" C HIS E 450 " pdb=" N PHE E 451 " pdb=" CA PHE E 451 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ALA P 214 " pdb=" C ALA P 214 " pdb=" N ILE P 215 " pdb=" CA ILE P 215 " ideal model delta harmonic sigma weight residual 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 24661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 4089 0.031 - 0.061: 1344 0.061 - 0.092: 384 0.092 - 0.122: 284 0.122 - 0.153: 35 Chirality restraints: 6136 Sorted by residual: chirality pdb=" CA MET A 485 " pdb=" N MET A 485 " pdb=" C MET A 485 " pdb=" CB MET A 485 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE N 11 " pdb=" N ILE N 11 " pdb=" C ILE N 11 " pdb=" CB ILE N 11 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE N 28 " pdb=" N ILE N 28 " pdb=" C ILE N 28 " pdb=" CB ILE N 28 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 6133 not shown) Planarity restraints: 7056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA P 119 " 0.064 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO P 120 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO P 120 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO P 120 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 468 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO F 469 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO F 469 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 469 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 87 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C LYS I 87 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS I 87 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL I 88 " -0.012 2.00e-02 2.50e+03 ... (remaining 7053 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 421 2.49 - 3.09: 32480 3.09 - 3.69: 60318 3.69 - 4.30: 84711 4.30 - 4.90: 139796 Nonbonded interactions: 317726 Sorted by model distance: nonbonded pdb=" OG1 THR N 58 " pdb=" OE1 GLU N 59 " model vdw 1.886 2.440 nonbonded pdb=" O ARG I 85 " pdb=" OG SER I 90 " model vdw 1.900 2.440 nonbonded pdb=" OD1 ASP N 13 " pdb=" OG1 THR N 16 " model vdw 1.928 2.440 nonbonded pdb=" OG SER C 93 " pdb=" OG1 THR C 214 " model vdw 1.955 2.440 nonbonded pdb=" O LEU D 266 " pdb=" OG1 THR D 270 " model vdw 1.972 2.440 ... (remaining 317721 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' selection = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 9 through 195 or resid 207 through 487)) selection = chain 'D' selection = (chain 'F' and (resid 9 through 195 or resid 207 through 487)) } ncs_group { reference = (chain 'G' and resid 31 through 232) selection = (chain 'I' and resid 31 through 232) selection = (chain 'K' and (resid 31 through 231 or (resid 232 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'H' selection = chain 'J' } 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 group one per residue 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.220 Construct map_model_manager: 0.030 Extract box with map and model: 15.190 Check model and map are aligned: 0.560 Set scattering table: 0.340 Process input model: 99.210 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.240 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.002 0.043 40247 Z= 0.162 Angle : 0.516 7.622 54373 Z= 0.286 Chirality : 0.039 0.153 6136 Planarity : 0.003 0.097 7056 Dihedral : 12.573 89.053 15248 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % 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: -0.28 (0.13), residues: 5003 helix: 1.66 (0.11), residues: 2205 sheet: -2.15 (0.23), residues: 542 loop : -1.59 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP O 303 HIS 0.008 0.001 HIS P 241 PHE 0.013 0.001 PHE E 258 TYR 0.018 0.001 TYR K 43 ARG 0.004 0.000 ARG N 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 488 time to evaluate : 4.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 29 LYS cc_start: 0.4576 (tppt) cc_final: 0.4173 (mmtt) REVERT: O 53 PHE cc_start: 0.5899 (m-80) cc_final: 0.4814 (m-80) REVERT: O 116 TRP cc_start: 0.6879 (t-100) cc_final: 0.5999 (t-100) REVERT: O 130 LEU cc_start: 0.8516 (mt) cc_final: 0.8309 (mt) REVERT: O 152 TYR cc_start: 0.8490 (t80) cc_final: 0.7828 (t80) REVERT: O 327 ILE cc_start: 0.4876 (mp) cc_final: 0.4659 (mt) REVERT: O 339 LYS cc_start: 0.5375 (tmmt) cc_final: 0.4728 (ptmt) REVERT: O 388 TYR cc_start: 0.5216 (m-80) cc_final: 0.4121 (m-80) REVERT: G 11 ASN cc_start: 0.6924 (p0) cc_final: 0.6616 (t0) REVERT: G 15 ASP cc_start: 0.6610 (m-30) cc_final: 0.6408 (m-30) REVERT: G 20 MET cc_start: 0.5159 (mtp) cc_final: 0.4525 (mtt) REVERT: G 23 PHE cc_start: 0.3114 (p90) cc_final: 0.2873 (p90) REVERT: G 43 TYR cc_start: 0.8078 (t80) cc_final: 0.7656 (t80) REVERT: G 152 MET cc_start: 0.6623 (ptt) cc_final: 0.6423 (ptt) REVERT: G 181 LYS cc_start: 0.4694 (mmtm) cc_final: 0.4394 (mmtm) REVERT: H 23 LYS cc_start: 0.8545 (tmmt) cc_final: 0.8252 (tptt) REVERT: H 57 PHE cc_start: 0.8390 (t80) cc_final: 0.7682 (t80) REVERT: B 317 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8165 (tp30) REVERT: B 383 MET cc_start: 0.9396 (ttm) cc_final: 0.9003 (ttm) REVERT: C 324 MET cc_start: 0.8754 (mmp) cc_final: 0.7952 (mpp) REVERT: D 150 MET cc_start: 0.8649 (tmm) cc_final: 0.8077 (tmm) REVERT: D 161 MET cc_start: 0.9053 (mpp) cc_final: 0.8719 (mpp) REVERT: D 383 MET cc_start: 0.8731 (ttp) cc_final: 0.8380 (ttp) REVERT: E 295 MET cc_start: 0.8156 (ppp) cc_final: 0.7934 (ppp) REVERT: E 352 MET cc_start: 0.8961 (tmm) cc_final: 0.8403 (tmm) REVERT: E 374 MET cc_start: 0.9104 (tpp) cc_final: 0.7970 (tpp) REVERT: E 546 MET cc_start: 0.9269 (ttp) cc_final: 0.8942 (ttm) REVERT: E 611 PHE cc_start: 0.7786 (m-80) cc_final: 0.7146 (m-80) REVERT: F 207 ASN cc_start: 0.7516 (m-40) cc_final: 0.7258 (t0) REVERT: F 280 ASP cc_start: 0.8559 (t0) cc_final: 0.8266 (m-30) REVERT: K 70 MET cc_start: 0.8461 (tmm) cc_final: 0.8242 (ttp) REVERT: L 61 ASN cc_start: 0.7506 (p0) cc_final: 0.6971 (p0) REVERT: M 118 ASN cc_start: 0.6048 (p0) cc_final: 0.5643 (m-40) REVERT: M 139 TYR cc_start: 0.7333 (t80) cc_final: 0.7116 (t80) REVERT: N 53 LYS cc_start: 0.7970 (mmmt) cc_final: 0.7466 (ptmm) REVERT: J 18 HIS cc_start: 0.8665 (m90) cc_final: 0.8305 (m170) REVERT: J 26 LYS cc_start: 0.8902 (mppt) cc_final: 0.8563 (pttp) REVERT: P 91 ARG cc_start: 0.8272 (tpt170) cc_final: 0.7904 (tpm170) REVERT: P 96 THR cc_start: 0.3301 (m) cc_final: 0.2784 (m) REVERT: P 105 GLU cc_start: 0.8313 (tp30) cc_final: 0.8018 (tp30) REVERT: P 112 HIS cc_start: 0.8664 (t-170) cc_final: 0.8284 (t-90) REVERT: P 260 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8290 (mmmm) outliers start: 0 outliers final: 0 residues processed: 488 average time/residue: 0.6020 time to fit residues: 462.5258 Evaluate side-chains 248 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 4.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 421 optimal weight: 20.0000 chunk 378 optimal weight: 8.9990 chunk 209 optimal weight: 7.9990 chunk 129 optimal weight: 0.5980 chunk 255 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 391 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 237 optimal weight: 9.9990 chunk 291 optimal weight: 6.9990 chunk 453 optimal weight: 9.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 18 GLN O 35 ASN O 87 GLN ** O 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 ASN ** O 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 282 GLN ** O 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS C 248 GLN C 349 ASN ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 GLN F 396 HIS M 78 ASN I 49 ASN ** I 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 40247 Z= 0.485 Angle : 0.748 10.202 54373 Z= 0.394 Chirality : 0.047 0.302 6136 Planarity : 0.005 0.072 7056 Dihedral : 4.906 33.029 5459 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.00 % Allowed : 8.45 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.12), residues: 5003 helix: 1.21 (0.11), residues: 2242 sheet: -2.14 (0.22), residues: 555 loop : -1.55 (0.14), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 567 HIS 0.007 0.002 HIS C 213 PHE 0.039 0.002 PHE K 62 TYR 0.041 0.002 TYR I 43 ARG 0.020 0.001 ARG P 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 247 time to evaluate : 4.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 327 ILE cc_start: 0.5414 (mp) cc_final: 0.5196 (mt) REVERT: G 11 ASN cc_start: 0.6913 (p0) cc_final: 0.6520 (t0) REVERT: G 152 MET cc_start: 0.6826 (ptt) cc_final: 0.6568 (ptt) REVERT: H 23 LYS cc_start: 0.8498 (tmmt) cc_final: 0.8151 (tptt) REVERT: B 337 MET cc_start: 0.9376 (mtm) cc_final: 0.9007 (mtp) REVERT: B 383 MET cc_start: 0.9380 (ttm) cc_final: 0.8913 (ttm) REVERT: C 45 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8310 (tpp) REVERT: C 324 MET cc_start: 0.8599 (mmp) cc_final: 0.7871 (mpp) REVERT: C 607 MET cc_start: 0.9308 (ptm) cc_final: 0.8720 (ppp) REVERT: D 150 MET cc_start: 0.8683 (tmm) cc_final: 0.8131 (tmm) REVERT: D 161 MET cc_start: 0.9205 (mpp) cc_final: 0.8798 (mpp) REVERT: D 383 MET cc_start: 0.8796 (ttp) cc_final: 0.8466 (ttp) REVERT: E 324 MET cc_start: 0.9456 (mtt) cc_final: 0.9128 (mtt) REVERT: F 391 MET cc_start: 0.8816 (pmm) cc_final: 0.8522 (pmm) REVERT: N 47 LYS cc_start: 0.6911 (tmtt) cc_final: 0.6492 (mmmt) REVERT: I 21 GLN cc_start: 0.8517 (tp-100) cc_final: 0.8118 (pt0) REVERT: I 157 MET cc_start: 0.8773 (mmt) cc_final: 0.8568 (mmt) REVERT: J 18 HIS cc_start: 0.8644 (m90) cc_final: 0.8201 (m170) REVERT: P 72 LYS cc_start: 0.6614 (mmmt) cc_final: 0.6195 (mmmt) REVERT: P 91 ARG cc_start: 0.8446 (tpt170) cc_final: 0.7777 (tpm170) REVERT: P 105 GLU cc_start: 0.8287 (tp30) cc_final: 0.8065 (tp30) REVERT: P 112 HIS cc_start: 0.8650 (t-170) cc_final: 0.8288 (t-90) REVERT: P 224 MET cc_start: 0.8859 (mmp) cc_final: 0.8521 (mmp) REVERT: P 260 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8373 (mmmm) outliers start: 43 outliers final: 26 residues processed: 276 average time/residue: 0.4923 time to fit residues: 226.4933 Evaluate side-chains 221 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 4.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 129 ASP Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 524 ASP Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 251 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 377 optimal weight: 5.9990 chunk 308 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 453 optimal weight: 9.9990 chunk 490 optimal weight: 20.0000 chunk 404 optimal weight: 1.9990 chunk 450 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 364 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 ASN ** O 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 324 HIS G 56 ASN C 248 GLN C 349 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 GLN ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 40247 Z= 0.243 Angle : 0.597 10.684 54373 Z= 0.315 Chirality : 0.043 0.234 6136 Planarity : 0.004 0.053 7056 Dihedral : 4.662 34.521 5459 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.60 % Allowed : 10.42 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.12), residues: 5003 helix: 1.45 (0.11), residues: 2239 sheet: -1.93 (0.22), residues: 570 loop : -1.38 (0.14), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 303 HIS 0.006 0.001 HIS O 274 PHE 0.041 0.001 PHE K 62 TYR 0.038 0.001 TYR I 43 ARG 0.011 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 226 time to evaluate : 4.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 116 TRP cc_start: 0.7133 (t-100) cc_final: 0.6929 (t-100) REVERT: G 11 ASN cc_start: 0.6936 (p0) cc_final: 0.6558 (t0) REVERT: H 23 LYS cc_start: 0.8509 (tmmt) cc_final: 0.8155 (tptt) REVERT: A 297 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.8593 (t80) REVERT: B 383 MET cc_start: 0.9269 (ttm) cc_final: 0.8836 (ttm) REVERT: C 45 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8366 (tpp) REVERT: C 324 MET cc_start: 0.8463 (mmp) cc_final: 0.7746 (mpp) REVERT: C 374 MET cc_start: 0.8863 (tpp) cc_final: 0.8651 (tpp) REVERT: C 604 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.8931 (tt) REVERT: C 607 MET cc_start: 0.9319 (ptm) cc_final: 0.8746 (ppp) REVERT: D 150 MET cc_start: 0.8740 (tmm) cc_final: 0.7944 (tmm) REVERT: D 161 MET cc_start: 0.9148 (mpp) cc_final: 0.8715 (mpp) REVERT: D 383 MET cc_start: 0.8775 (ttp) cc_final: 0.8375 (ttp) REVERT: E 324 MET cc_start: 0.9330 (mtt) cc_final: 0.8963 (mtt) REVERT: E 607 MET cc_start: 0.8566 (ptm) cc_final: 0.8275 (ppp) REVERT: F 391 MET cc_start: 0.8791 (pmm) cc_final: 0.8475 (pmm) REVERT: K 157 MET cc_start: 0.8895 (mmm) cc_final: 0.8612 (mmm) REVERT: N 47 LYS cc_start: 0.6964 (tmtt) cc_final: 0.6486 (mmmt) REVERT: I 21 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8133 (pt0) REVERT: I 52 ARG cc_start: 0.8865 (mmp-170) cc_final: 0.8470 (mmp-170) REVERT: I 157 MET cc_start: 0.8659 (mmt) cc_final: 0.8137 (mmt) REVERT: J 18 HIS cc_start: 0.8683 (m90) cc_final: 0.7840 (m170) REVERT: P 91 ARG cc_start: 0.8497 (tpt170) cc_final: 0.7804 (tpm170) REVERT: P 156 ARG cc_start: 0.7969 (ptp-170) cc_final: 0.7628 (ptp-170) REVERT: P 224 MET cc_start: 0.8897 (mmp) cc_final: 0.8662 (mmp) REVERT: P 260 LYS cc_start: 0.8669 (mmmt) cc_final: 0.8468 (mmmm) outliers start: 69 outliers final: 39 residues processed: 277 average time/residue: 0.4737 time to fit residues: 222.2285 Evaluate side-chains 241 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 199 time to evaluate : 4.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain J residue 59 GLN Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 237 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 448 optimal weight: 0.0370 chunk 341 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 216 optimal weight: 4.9990 chunk 304 optimal weight: 9.9990 chunk 455 optimal weight: 10.0000 chunk 482 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 431 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 40247 Z= 0.355 Angle : 0.646 10.278 54373 Z= 0.339 Chirality : 0.044 0.180 6136 Planarity : 0.004 0.057 7056 Dihedral : 4.786 34.467 5459 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.21 % Allowed : 12.72 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.12), residues: 5003 helix: 1.36 (0.11), residues: 2238 sheet: -1.89 (0.21), residues: 581 loop : -1.47 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 303 HIS 0.007 0.001 HIS H 18 PHE 0.034 0.002 PHE K 62 TYR 0.038 0.002 TYR I 43 ARG 0.006 0.000 ARG H 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 203 time to evaluate : 4.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 104 ASN cc_start: 0.7609 (OUTLIER) cc_final: 0.7209 (m-40) REVERT: G 11 ASN cc_start: 0.7000 (p0) cc_final: 0.6614 (t0) REVERT: H 23 LYS cc_start: 0.8512 (tmmt) cc_final: 0.8074 (tptt) REVERT: A 297 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.8660 (t80) REVERT: A 312 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7808 (mpp) REVERT: A 352 MET cc_start: 0.8785 (ttt) cc_final: 0.8560 (ttt) REVERT: B 337 MET cc_start: 0.9389 (mtm) cc_final: 0.9020 (mtp) REVERT: B 383 MET cc_start: 0.9259 (ttm) cc_final: 0.8652 (ttm) REVERT: C 45 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8352 (tpp) REVERT: C 324 MET cc_start: 0.8618 (mmp) cc_final: 0.7874 (mpp) REVERT: C 604 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.8980 (tt) REVERT: C 607 MET cc_start: 0.9330 (ptm) cc_final: 0.8747 (ppp) REVERT: D 150 MET cc_start: 0.8719 (tmm) cc_final: 0.7899 (tmm) REVERT: D 161 MET cc_start: 0.9191 (mpp) cc_final: 0.8748 (mpp) REVERT: D 383 MET cc_start: 0.8866 (ttp) cc_final: 0.8450 (ttp) REVERT: D 472 MET cc_start: 0.8889 (mtt) cc_final: 0.8617 (mtt) REVERT: E 295 MET cc_start: 0.8653 (ppp) cc_final: 0.8365 (ppp) REVERT: E 324 MET cc_start: 0.9391 (mtt) cc_final: 0.8812 (mtt) REVERT: E 482 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.8898 (ptp90) REVERT: E 547 MET cc_start: 0.9182 (ptm) cc_final: 0.8891 (ptp) REVERT: F 391 MET cc_start: 0.8854 (pmm) cc_final: 0.8531 (pmm) REVERT: N 47 LYS cc_start: 0.6991 (tmtt) cc_final: 0.6520 (mmmt) REVERT: I 52 ARG cc_start: 0.8847 (mmp-170) cc_final: 0.8492 (mmp-170) REVERT: J 18 HIS cc_start: 0.8375 (m90) cc_final: 0.7930 (m170) REVERT: J 27 TYR cc_start: 0.7958 (m-10) cc_final: 0.7529 (m-80) REVERT: P 91 ARG cc_start: 0.8542 (tpt170) cc_final: 0.7819 (tpm170) REVERT: P 224 MET cc_start: 0.8950 (mmp) cc_final: 0.8740 (mmp) outliers start: 95 outliers final: 56 residues processed: 282 average time/residue: 0.4771 time to fit residues: 229.5493 Evaluate side-chains 248 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 186 time to evaluate : 4.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain O residue 129 ASP Chi-restraints excluded: chain O residue 210 TYR Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 574 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 178 TYR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 236 ASP Chi-restraints excluded: chain P residue 237 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 401 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 359 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 411 optimal weight: 1.9990 chunk 333 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 246 optimal weight: 0.9990 chunk 432 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 GLN I 94 GLN ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40247 Z= 0.198 Angle : 0.570 11.657 54373 Z= 0.299 Chirality : 0.042 0.259 6136 Planarity : 0.004 0.053 7056 Dihedral : 4.584 35.898 5459 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.90 % Allowed : 13.65 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.12), residues: 5003 helix: 1.53 (0.11), residues: 2243 sheet: -1.77 (0.21), residues: 585 loop : -1.38 (0.14), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 567 HIS 0.006 0.001 HIS H 18 PHE 0.024 0.001 PHE E 258 TYR 0.031 0.001 TYR I 43 ARG 0.003 0.000 ARG H 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 210 time to evaluate : 4.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 105 MET cc_start: 0.6961 (mmt) cc_final: 0.6324 (ppp) REVERT: G 11 ASN cc_start: 0.6906 (p0) cc_final: 0.6498 (t0) REVERT: H 23 LYS cc_start: 0.8487 (tmmt) cc_final: 0.8089 (tptt) REVERT: A 297 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.8670 (t80) REVERT: B 337 MET cc_start: 0.9326 (mtm) cc_final: 0.9006 (mtp) REVERT: B 383 MET cc_start: 0.9228 (ttm) cc_final: 0.8639 (ttm) REVERT: C 45 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8442 (tpp) REVERT: C 324 MET cc_start: 0.8518 (mmp) cc_final: 0.7768 (mpp) REVERT: C 604 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.8925 (tt) REVERT: C 607 MET cc_start: 0.9324 (ptm) cc_final: 0.8760 (ppp) REVERT: D 150 MET cc_start: 0.8769 (tmm) cc_final: 0.7978 (tmm) REVERT: D 151 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8781 (tp) REVERT: D 161 MET cc_start: 0.9152 (mpp) cc_final: 0.8644 (mpp) REVERT: D 383 MET cc_start: 0.8802 (ttp) cc_final: 0.8380 (ttp) REVERT: D 472 MET cc_start: 0.8874 (mtt) cc_final: 0.8595 (mtt) REVERT: E 324 MET cc_start: 0.9390 (mtt) cc_final: 0.8857 (mtt) REVERT: E 348 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8986 (mtpp) REVERT: E 547 MET cc_start: 0.9136 (ptm) cc_final: 0.8823 (ptp) REVERT: F 391 MET cc_start: 0.8795 (pmm) cc_final: 0.8476 (pmm) REVERT: F 419 VAL cc_start: 0.8950 (t) cc_final: 0.8745 (t) REVERT: M 13 MET cc_start: 0.5489 (mmm) cc_final: 0.5060 (mmm) REVERT: M 118 ASN cc_start: 0.6447 (p0) cc_final: 0.5932 (m-40) REVERT: N 47 LYS cc_start: 0.6987 (tmtt) cc_final: 0.6518 (mmmt) REVERT: I 21 GLN cc_start: 0.8638 (tp-100) cc_final: 0.8061 (pt0) REVERT: I 52 ARG cc_start: 0.8835 (mmp-170) cc_final: 0.8472 (mmp-170) REVERT: J 18 HIS cc_start: 0.8348 (m90) cc_final: 0.7897 (m170) REVERT: J 53 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7578 (pp20) REVERT: P 72 LYS cc_start: 0.6612 (mmmt) cc_final: 0.6274 (mmtm) REVERT: P 91 ARG cc_start: 0.8562 (tpt170) cc_final: 0.7844 (tpm170) REVERT: P 157 GLN cc_start: 0.6578 (mp10) cc_final: 0.6369 (mp10) REVERT: P 224 MET cc_start: 0.8949 (mmp) cc_final: 0.8691 (mmp) outliers start: 82 outliers final: 49 residues processed: 279 average time/residue: 0.5035 time to fit residues: 238.2982 Evaluate side-chains 246 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 191 time to evaluate : 4.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 348 LYS Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 236 ASP Chi-restraints excluded: chain P residue 237 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 162 optimal weight: 0.9980 chunk 434 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 482 optimal weight: 6.9990 chunk 400 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 253 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 40247 Z= 0.380 Angle : 0.652 14.238 54373 Z= 0.341 Chirality : 0.044 0.198 6136 Planarity : 0.004 0.057 7056 Dihedral : 4.764 35.303 5459 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.69 % Allowed : 14.23 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.34 (0.12), residues: 5003 helix: 1.37 (0.11), residues: 2246 sheet: -1.81 (0.21), residues: 598 loop : -1.47 (0.14), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 98 HIS 0.006 0.001 HIS H 18 PHE 0.025 0.002 PHE E 258 TYR 0.034 0.002 TYR I 43 ARG 0.004 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 194 time to evaluate : 4.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 105 MET cc_start: 0.6808 (mmt) cc_final: 0.6258 (ppp) REVERT: O 244 GLN cc_start: 0.5477 (OUTLIER) cc_final: 0.5172 (pp30) REVERT: G 11 ASN cc_start: 0.6948 (p0) cc_final: 0.6581 (t0) REVERT: H 23 LYS cc_start: 0.8513 (tmmt) cc_final: 0.8093 (tptt) REVERT: A 297 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8785 (t80) REVERT: B 289 ARG cc_start: 0.9432 (OUTLIER) cc_final: 0.9059 (ptp-110) REVERT: B 337 MET cc_start: 0.9410 (mtm) cc_final: 0.9139 (mtp) REVERT: B 383 MET cc_start: 0.9268 (ttm) cc_final: 0.8588 (ttm) REVERT: C 45 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8392 (tpp) REVERT: C 101 MET cc_start: 0.9011 (tpp) cc_final: 0.8790 (tpp) REVERT: C 312 MET cc_start: 0.9376 (mmm) cc_final: 0.8278 (tpp) REVERT: C 471 TYR cc_start: 0.9361 (OUTLIER) cc_final: 0.8944 (m-80) REVERT: C 604 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.8985 (tt) REVERT: C 607 MET cc_start: 0.9354 (ptm) cc_final: 0.8770 (ppp) REVERT: D 150 MET cc_start: 0.8784 (tmm) cc_final: 0.7965 (tmm) REVERT: D 151 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8811 (tp) REVERT: D 161 MET cc_start: 0.9243 (mpp) cc_final: 0.8871 (mpp) REVERT: D 383 MET cc_start: 0.8926 (ttp) cc_final: 0.8480 (ttp) REVERT: D 472 MET cc_start: 0.8878 (mtt) cc_final: 0.8475 (mtt) REVERT: E 324 MET cc_start: 0.9442 (mtt) cc_final: 0.8646 (mpp) REVERT: F 150 MET cc_start: 0.7990 (tmm) cc_final: 0.7671 (tmm) REVERT: M 13 MET cc_start: 0.5435 (mmm) cc_final: 0.5072 (mmm) REVERT: M 118 ASN cc_start: 0.6386 (p0) cc_final: 0.5793 (m-40) REVERT: N 47 LYS cc_start: 0.7118 (tmtt) cc_final: 0.6698 (mmmt) REVERT: I 52 ARG cc_start: 0.8878 (mmp-170) cc_final: 0.8496 (mmp-170) REVERT: I 82 ASN cc_start: 0.9255 (t0) cc_final: 0.8508 (p0) REVERT: J 18 HIS cc_start: 0.8319 (m90) cc_final: 0.7882 (m170) REVERT: J 53 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7493 (pp20) REVERT: P 91 ARG cc_start: 0.8580 (tpt170) cc_final: 0.7822 (tpm170) REVERT: P 112 HIS cc_start: 0.8590 (OUTLIER) cc_final: 0.8168 (t-90) REVERT: P 224 MET cc_start: 0.8909 (mmp) cc_final: 0.8536 (mmm) outliers start: 116 outliers final: 70 residues processed: 297 average time/residue: 0.4726 time to fit residues: 238.3557 Evaluate side-chains 262 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 183 time to evaluate : 4.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 210 TYR Chi-restraints excluded: chain O residue 244 GLN Chi-restraints excluded: chain O residue 339 LYS Chi-restraints excluded: chain O residue 350 PHE Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 574 THR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 467 ILE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 178 TYR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 112 HIS Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 236 ASP Chi-restraints excluded: chain P residue 237 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 465 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 275 optimal weight: 0.8980 chunk 352 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 406 optimal weight: 9.9990 chunk 269 optimal weight: 0.5980 chunk 480 optimal weight: 1.9990 chunk 300 optimal weight: 8.9990 chunk 293 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40247 Z= 0.191 Angle : 0.578 16.275 54373 Z= 0.301 Chirality : 0.043 0.197 6136 Planarity : 0.004 0.053 7056 Dihedral : 4.538 35.246 5459 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.00 % Allowed : 15.25 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.12), residues: 5003 helix: 1.54 (0.11), residues: 2256 sheet: -1.71 (0.22), residues: 553 loop : -1.35 (0.14), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 303 HIS 0.006 0.001 HIS H 18 PHE 0.043 0.001 PHE C 258 TYR 0.038 0.001 TYR J 27 ARG 0.006 0.000 ARG J 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 201 time to evaluate : 4.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 105 MET cc_start: 0.6696 (mmt) cc_final: 0.6165 (tmm) REVERT: O 244 GLN cc_start: 0.5596 (OUTLIER) cc_final: 0.5269 (pp30) REVERT: O 339 LYS cc_start: 0.3744 (OUTLIER) cc_final: 0.3445 (ptmm) REVERT: G 11 ASN cc_start: 0.7015 (p0) cc_final: 0.6654 (t0) REVERT: H 23 LYS cc_start: 0.8498 (tmmt) cc_final: 0.8068 (tptt) REVERT: A 45 MET cc_start: 0.8661 (tpp) cc_final: 0.8393 (tpp) REVERT: A 352 MET cc_start: 0.8690 (ttt) cc_final: 0.8273 (ttt) REVERT: A 546 MET cc_start: 0.9543 (mtm) cc_final: 0.8951 (mtt) REVERT: B 383 MET cc_start: 0.9235 (ttm) cc_final: 0.8522 (ttm) REVERT: C 45 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8437 (tpp) REVERT: C 324 MET cc_start: 0.8548 (mmp) cc_final: 0.7973 (mpp) REVERT: C 471 TYR cc_start: 0.9284 (OUTLIER) cc_final: 0.8889 (m-10) REVERT: C 546 MET cc_start: 0.9030 (ttm) cc_final: 0.8743 (ptm) REVERT: C 604 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.8920 (tt) REVERT: C 607 MET cc_start: 0.9327 (ptm) cc_final: 0.8752 (ppp) REVERT: D 150 MET cc_start: 0.8774 (tmm) cc_final: 0.7974 (tmm) REVERT: D 151 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8915 (tp) REVERT: D 161 MET cc_start: 0.9214 (mpp) cc_final: 0.8764 (mpp) REVERT: D 383 MET cc_start: 0.8834 (ttp) cc_final: 0.8414 (ttp) REVERT: D 472 MET cc_start: 0.8837 (mtt) cc_final: 0.8501 (mtt) REVERT: E 324 MET cc_start: 0.9391 (mtt) cc_final: 0.8627 (mpp) REVERT: E 348 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8998 (mtpp) REVERT: F 150 MET cc_start: 0.7983 (tmm) cc_final: 0.7664 (tmm) REVERT: F 215 MET cc_start: 0.9075 (pmm) cc_final: 0.8708 (pmm) REVERT: F 230 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8604 (tp30) REVERT: F 391 MET cc_start: 0.8686 (pmm) cc_final: 0.8448 (pmm) REVERT: M 13 MET cc_start: 0.5399 (mmm) cc_final: 0.5064 (mmm) REVERT: M 118 ASN cc_start: 0.6390 (p0) cc_final: 0.5805 (m-40) REVERT: M 193 ASP cc_start: 0.8848 (t0) cc_final: 0.8366 (p0) REVERT: N 47 LYS cc_start: 0.7133 (tmtt) cc_final: 0.6724 (mmmt) REVERT: I 82 ASN cc_start: 0.9187 (t0) cc_final: 0.8471 (p0) REVERT: J 18 HIS cc_start: 0.8295 (m90) cc_final: 0.7821 (m170) REVERT: J 53 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7554 (pp20) REVERT: P 72 LYS cc_start: 0.6421 (mmmt) cc_final: 0.6121 (mmtt) REVERT: P 91 ARG cc_start: 0.8625 (tpt170) cc_final: 0.7848 (tpm170) REVERT: P 224 MET cc_start: 0.8966 (mmp) cc_final: 0.8734 (mmp) outliers start: 86 outliers final: 60 residues processed: 277 average time/residue: 0.5031 time to fit residues: 236.8278 Evaluate side-chains 255 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 187 time to evaluate : 4.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 210 TYR Chi-restraints excluded: chain O residue 244 GLN Chi-restraints excluded: chain O residue 339 LYS Chi-restraints excluded: chain O residue 350 PHE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 348 LYS Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 574 THR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 112 HIS Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 236 ASP Chi-restraints excluded: chain P residue 237 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 297 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 287 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 305 optimal weight: 3.9990 chunk 327 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 378 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 HIS ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 40247 Z= 0.321 Angle : 0.632 14.577 54373 Z= 0.326 Chirality : 0.043 0.182 6136 Planarity : 0.004 0.053 7056 Dihedral : 4.660 35.346 5459 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.18 % Allowed : 15.58 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.20 (0.12), residues: 5003 helix: 1.49 (0.11), residues: 2245 sheet: -1.65 (0.21), residues: 590 loop : -1.44 (0.14), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 303 HIS 0.006 0.001 HIS H 18 PHE 0.026 0.002 PHE G 23 TYR 0.029 0.001 TYR I 43 ARG 0.006 0.000 ARG H 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 198 time to evaluate : 4.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 105 MET cc_start: 0.6689 (mmt) cc_final: 0.6163 (tmm) REVERT: O 119 ARG cc_start: 0.7959 (mmm-85) cc_final: 0.7457 (ttt180) REVERT: O 244 GLN cc_start: 0.5450 (OUTLIER) cc_final: 0.5163 (pp30) REVERT: O 339 LYS cc_start: 0.3726 (OUTLIER) cc_final: 0.3420 (ptmm) REVERT: G 11 ASN cc_start: 0.7028 (p0) cc_final: 0.6667 (t0) REVERT: H 23 LYS cc_start: 0.8429 (tmmt) cc_final: 0.7977 (tptt) REVERT: A 45 MET cc_start: 0.8753 (tpp) cc_final: 0.8444 (tpp) REVERT: A 297 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8786 (t80) REVERT: B 289 ARG cc_start: 0.9400 (OUTLIER) cc_final: 0.9057 (ptp-110) REVERT: B 383 MET cc_start: 0.9207 (ttm) cc_final: 0.8577 (ttm) REVERT: C 45 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8433 (tpp) REVERT: C 324 MET cc_start: 0.8704 (mmp) cc_final: 0.8027 (mpp) REVERT: C 471 TYR cc_start: 0.9338 (OUTLIER) cc_final: 0.8952 (m-10) REVERT: C 604 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.8930 (tt) REVERT: C 607 MET cc_start: 0.9347 (ptm) cc_final: 0.8763 (ppp) REVERT: D 150 MET cc_start: 0.8793 (tmm) cc_final: 0.7988 (tmm) REVERT: D 151 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8907 (tp) REVERT: D 161 MET cc_start: 0.9270 (mpp) cc_final: 0.8866 (mpp) REVERT: D 383 MET cc_start: 0.8927 (ttp) cc_final: 0.8466 (ttp) REVERT: D 472 MET cc_start: 0.8781 (mtt) cc_final: 0.8335 (mtt) REVERT: E 324 MET cc_start: 0.9425 (mtt) cc_final: 0.8609 (mpp) REVERT: F 230 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8703 (tp30) REVERT: F 391 MET cc_start: 0.8769 (pmm) cc_final: 0.8520 (pmm) REVERT: M 13 MET cc_start: 0.5404 (mmm) cc_final: 0.5159 (mmm) REVERT: M 118 ASN cc_start: 0.6405 (p0) cc_final: 0.5822 (m-40) REVERT: M 193 ASP cc_start: 0.8857 (t0) cc_final: 0.8389 (p0) REVERT: N 47 LYS cc_start: 0.7144 (tmtt) cc_final: 0.6703 (mmmt) REVERT: J 18 HIS cc_start: 0.8284 (m90) cc_final: 0.7827 (m170) REVERT: J 53 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7692 (pp20) REVERT: P 91 ARG cc_start: 0.8644 (tpt170) cc_final: 0.7857 (tpm170) REVERT: P 224 MET cc_start: 0.8955 (mmp) cc_final: 0.8570 (mmm) outliers start: 94 outliers final: 72 residues processed: 282 average time/residue: 0.4949 time to fit residues: 232.6883 Evaluate side-chains 269 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 188 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 210 TYR Chi-restraints excluded: chain O residue 244 GLN Chi-restraints excluded: chain O residue 339 LYS Chi-restraints excluded: chain O residue 350 PHE Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 574 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 467 ILE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 178 TYR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 112 HIS Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 236 ASP Chi-restraints excluded: chain P residue 237 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 437 optimal weight: 30.0000 chunk 460 optimal weight: 7.9990 chunk 420 optimal weight: 8.9990 chunk 448 optimal weight: 10.0000 chunk 269 optimal weight: 0.7980 chunk 195 optimal weight: 0.0970 chunk 351 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 chunk 405 optimal weight: 0.9980 chunk 423 optimal weight: 1.9990 chunk 446 optimal weight: 20.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 73 ASN ** O 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 274 HIS ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 HIS N 55 ASN N 70 ASN P 252 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 40247 Z= 0.161 Angle : 0.577 13.228 54373 Z= 0.298 Chirality : 0.042 0.239 6136 Planarity : 0.004 0.050 7056 Dihedral : 4.424 35.490 5459 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.60 % Allowed : 16.39 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.02 (0.12), residues: 5003 helix: 1.57 (0.11), residues: 2261 sheet: -1.57 (0.22), residues: 571 loop : -1.30 (0.14), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 567 HIS 0.006 0.001 HIS H 18 PHE 0.034 0.001 PHE K 62 TYR 0.025 0.001 TYR I 43 ARG 0.008 0.000 ARG O 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 206 time to evaluate : 4.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 119 ARG cc_start: 0.7886 (mmm-85) cc_final: 0.7341 (ttt180) REVERT: O 339 LYS cc_start: 0.3774 (OUTLIER) cc_final: 0.3475 (ptmm) REVERT: G 11 ASN cc_start: 0.7087 (p0) cc_final: 0.6744 (t0) REVERT: H 23 LYS cc_start: 0.8486 (tmmt) cc_final: 0.8068 (tptt) REVERT: A 45 MET cc_start: 0.8688 (tpp) cc_final: 0.8435 (tpp) REVERT: A 607 MET cc_start: 0.9126 (ptt) cc_final: 0.8839 (ppp) REVERT: B 289 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.8986 (ptp-110) REVERT: C 45 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8386 (tpp) REVERT: C 290 MET cc_start: 0.9221 (mmm) cc_final: 0.8666 (tpp) REVERT: C 324 MET cc_start: 0.8537 (mmp) cc_final: 0.7909 (mpp) REVERT: C 471 TYR cc_start: 0.9261 (OUTLIER) cc_final: 0.8872 (m-10) REVERT: C 546 MET cc_start: 0.8988 (ttm) cc_final: 0.8780 (ptm) REVERT: C 607 MET cc_start: 0.9330 (ptm) cc_final: 0.8729 (ppp) REVERT: D 150 MET cc_start: 0.8798 (tmm) cc_final: 0.8015 (tmm) REVERT: D 151 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8895 (tp) REVERT: D 161 MET cc_start: 0.9235 (mpp) cc_final: 0.8809 (mpp) REVERT: D 383 MET cc_start: 0.8825 (ttp) cc_final: 0.8410 (ttp) REVERT: D 472 MET cc_start: 0.8772 (mtt) cc_final: 0.8422 (mtt) REVERT: E 324 MET cc_start: 0.9351 (mtt) cc_final: 0.8661 (mpp) REVERT: F 230 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8576 (tp30) REVERT: M 13 MET cc_start: 0.5348 (mmm) cc_final: 0.5103 (mmm) REVERT: M 118 ASN cc_start: 0.6346 (p0) cc_final: 0.5779 (m-40) REVERT: M 193 ASP cc_start: 0.8822 (t0) cc_final: 0.8364 (p0) REVERT: N 47 LYS cc_start: 0.7006 (tmtt) cc_final: 0.6531 (mmmt) REVERT: I 157 MET cc_start: 0.8521 (mmt) cc_final: 0.8053 (mmt) REVERT: J 53 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7667 (pp20) REVERT: P 91 ARG cc_start: 0.8694 (tpt170) cc_final: 0.7871 (tpm170) REVERT: P 224 MET cc_start: 0.8984 (mmp) cc_final: 0.8719 (mmp) outliers start: 69 outliers final: 56 residues processed: 266 average time/residue: 0.4867 time to fit residues: 219.4460 Evaluate side-chains 255 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 193 time to evaluate : 4.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 210 TYR Chi-restraints excluded: chain O residue 339 LYS Chi-restraints excluded: chain O residue 350 PHE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 574 THR Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 467 ILE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 236 ASP Chi-restraints excluded: chain P residue 237 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 294 optimal weight: 9.9990 chunk 473 optimal weight: 6.9990 chunk 289 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 329 optimal weight: 9.9990 chunk 497 optimal weight: 9.9990 chunk 457 optimal weight: 8.9990 chunk 395 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 242 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 GLN E 109 GLN ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 40247 Z= 0.524 Angle : 0.780 14.024 54373 Z= 0.404 Chirality : 0.046 0.247 6136 Planarity : 0.005 0.057 7056 Dihedral : 4.978 35.459 5459 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 1.97 % Allowed : 16.37 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.51 (0.12), residues: 5003 helix: 1.18 (0.11), residues: 2250 sheet: -1.76 (0.21), residues: 572 loop : -1.56 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 215 HIS 0.009 0.002 HIS B 344 PHE 0.034 0.002 PHE F 439 TYR 0.031 0.002 TYR I 43 ARG 0.009 0.001 ARG H 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 191 time to evaluate : 4.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 244 GLN cc_start: 0.5460 (OUTLIER) cc_final: 0.5138 (pp30) REVERT: O 339 LYS cc_start: 0.3825 (OUTLIER) cc_final: 0.3486 (ptmm) REVERT: G 11 ASN cc_start: 0.7064 (p0) cc_final: 0.6723 (t0) REVERT: H 23 LYS cc_start: 0.8343 (tmmt) cc_final: 0.7841 (tptt) REVERT: A 45 MET cc_start: 0.8805 (tpp) cc_final: 0.8474 (tpp) REVERT: A 607 MET cc_start: 0.9170 (ptt) cc_final: 0.8896 (ppp) REVERT: B 289 ARG cc_start: 0.9414 (OUTLIER) cc_final: 0.9008 (ptp-110) REVERT: B 383 MET cc_start: 0.9240 (ttm) cc_final: 0.8763 (ttm) REVERT: C 45 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8393 (tpp) REVERT: C 290 MET cc_start: 0.9264 (mmm) cc_final: 0.8792 (tpp) REVERT: C 324 MET cc_start: 0.8867 (mmp) cc_final: 0.8119 (mpp) REVERT: C 471 TYR cc_start: 0.9389 (OUTLIER) cc_final: 0.8983 (m-80) REVERT: C 604 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.8933 (tt) REVERT: C 607 MET cc_start: 0.9356 (ptm) cc_final: 0.8747 (ppp) REVERT: D 150 MET cc_start: 0.8765 (tmm) cc_final: 0.7904 (tmm) REVERT: D 151 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8871 (tp) REVERT: D 161 MET cc_start: 0.9327 (mpp) cc_final: 0.9014 (mpp) REVERT: D 383 MET cc_start: 0.8991 (ttp) cc_final: 0.8567 (ttp) REVERT: D 472 MET cc_start: 0.8895 (mtt) cc_final: 0.8412 (mtt) REVERT: E 324 MET cc_start: 0.9469 (mtt) cc_final: 0.8612 (mpp) REVERT: F 230 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8546 (tp30) REVERT: M 13 MET cc_start: 0.5424 (mmm) cc_final: 0.5175 (mmm) REVERT: M 118 ASN cc_start: 0.6258 (p0) cc_final: 0.5754 (m-40) REVERT: M 193 ASP cc_start: 0.8830 (t0) cc_final: 0.8491 (p0) REVERT: N 47 LYS cc_start: 0.7068 (tmtt) cc_final: 0.6628 (mmmt) REVERT: J 34 GLN cc_start: 0.8428 (pt0) cc_final: 0.8107 (pp30) REVERT: J 53 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7600 (pp20) REVERT: P 224 MET cc_start: 0.8927 (mmp) cc_final: 0.8532 (mmm) outliers start: 85 outliers final: 69 residues processed: 267 average time/residue: 0.4874 time to fit residues: 220.7196 Evaluate side-chains 265 residues out of total 4323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 188 time to evaluate : 4.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 210 TYR Chi-restraints excluded: chain O residue 244 GLN Chi-restraints excluded: chain O residue 339 LYS Chi-restraints excluded: chain O residue 350 PHE Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 361 ASP Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 574 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 178 TYR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 112 HIS Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 236 ASP Chi-restraints excluded: chain P residue 237 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 314 optimal weight: 0.8980 chunk 421 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 365 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 396 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 407 optimal weight: 10.0000 chunk 50 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 GLN E 109 GLN P 230 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.068289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.047143 restraints weight = 218787.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.048174 restraints weight = 116629.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.048805 restraints weight = 78331.811| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40247 Z= 0.164 Angle : 0.599 13.186 54373 Z= 0.310 Chirality : 0.043 0.230 6136 Planarity : 0.004 0.050 7056 Dihedral : 4.524 35.613 5459 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.53 % Allowed : 16.95 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.09 (0.12), residues: 5003 helix: 1.50 (0.11), residues: 2267 sheet: -1.53 (0.22), residues: 569 loop : -1.36 (0.14), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 567 HIS 0.008 0.001 HIS P 230 PHE 0.029 0.001 PHE K 62 TYR 0.026 0.001 TYR I 43 ARG 0.014 0.000 ARG P 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6800.70 seconds wall clock time: 125 minutes 46.47 seconds (7546.47 seconds total)