Starting phenix.real_space_refine on Wed Mar 20 14:21:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/03_2024/6v4j_21041_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/03_2024/6v4j_21041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/03_2024/6v4j_21041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/03_2024/6v4j_21041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/03_2024/6v4j_21041_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4j_21041/03_2024/6v4j_21041_neut.pdb" } resolution = 2.97 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= 0.006 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 7018 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 105 5.16 5 C 13526 2.51 5 N 3346 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 76": "OD1" <-> "OD2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 283": "OD1" <-> "OD2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "F ASP 76": "OD1" <-> "OD2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 307": "OE1" <-> "OE2" Residue "F TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 76": "OD1" <-> "OD2" Residue "G PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 308": "OD1" <-> "OD2" Residue "H ARG 332": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20637 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3450 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 17, 'TRANS': 429} Chain breaks: 5 Chain: "B" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3354 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 16, 'TRANS': 417} Chain breaks: 6 Chain: "C" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3414 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 424} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3390 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 17, 'TRANS': 420} Chain breaks: 5 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1748 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1767 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 2 Chain: "G" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1753 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1761 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.08, per 1000 atoms: 0.49 Number of scatterers: 20637 At special positions: 0 Unit cell: (120.474, 177.606, 109.296, 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 105 16.00 O 3660 8.00 N 3346 7.00 C 13526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 348 " distance=2.05 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 348 " distance=1.59 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 348 " distance=2.04 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: 7.21 Conformation dependent library (CDL) restraints added in 3.4 seconds 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4974 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 8 sheets defined 62.8% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 2 through 20 removed outlier: 3.772A pdb=" N ILE A 6 " --> pdb=" O GLN A 2 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG A 8 " --> pdb=" O ARG A 4 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 22 No H-bonds generated for 'chain 'A' and resid 21 through 22' Processing helix chain 'A' and resid 23 through 27 removed outlier: 3.727A pdb=" N LEU A 26 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 48 removed outlier: 3.781A pdb=" N LEU A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.739A pdb=" N LEU A 89 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 124 through 149 removed outlier: 3.731A pdb=" N MET A 140 " --> pdb=" O TRP A 136 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 202 removed outlier: 4.517A pdb=" N ALA A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 235 through 252 removed outlier: 3.968A pdb=" N CYS A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 4.114A pdb=" N ALA A 258 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 273 through 298 removed outlier: 4.063A pdb=" N ARG A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 319 Processing helix chain 'A' and resid 333 through 345 removed outlier: 4.560A pdb=" N VAL A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 377 Processing helix chain 'A' and resid 392 through 420 removed outlier: 4.133A pdb=" N VAL A 396 " --> pdb=" O PRO A 392 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 442 through 446 removed outlier: 4.107A pdb=" N ALA A 446 " --> pdb=" O GLY A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 471 through 479 removed outlier: 4.152A pdb=" N LEU A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 20 removed outlier: 3.594A pdb=" N ILE B 6 " --> pdb=" O GLN B 2 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 22 No H-bonds generated for 'chain 'B' and resid 21 through 22' Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.575A pdb=" N LEU B 26 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 55 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 78 through 82 removed outlier: 4.099A pdb=" N GLY B 81 " --> pdb=" O THR B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.688A pdb=" N LEU B 89 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 124 through 149 removed outlier: 3.652A pdb=" N ILE B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 203 removed outlier: 4.495A pdb=" N ALA B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 235 through 251 removed outlier: 3.598A pdb=" N ALA B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N CYS B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 4.083A pdb=" N ALA B 258 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 298 Processing helix chain 'B' and resid 302 through 319 removed outlier: 3.520A pdb=" N ALA B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.731A pdb=" N ILE B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 392 through 420 removed outlier: 4.105A pdb=" N VAL B 396 " --> pdb=" O PRO B 392 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 437 Processing helix chain 'B' and resid 453 through 469 Processing helix chain 'B' and resid 471 through 479 removed outlier: 3.651A pdb=" N LEU B 475 " --> pdb=" O ILE B 471 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.738A pdb=" N ILE C 6 " --> pdb=" O GLN C 2 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG C 8 " --> pdb=" O ARG C 4 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.722A pdb=" N LEU C 26 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 53 Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.818A pdb=" N LEU C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.720A pdb=" N LEU C 89 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 111 removed outlier: 3.896A pdb=" N THR C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.732A pdb=" N ILE C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 203 removed outlier: 4.409A pdb=" N ALA C 184 " --> pdb=" O GLU C 180 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 235 through 251 removed outlier: 4.070A pdb=" N CYS C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 removed outlier: 4.147A pdb=" N ALA C 258 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 268 through 273 Processing helix chain 'C' and resid 273 through 298 removed outlier: 3.941A pdb=" N ARG C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 319 removed outlier: 3.724A pdb=" N ALA C 306 " --> pdb=" O SER C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 removed outlier: 3.710A pdb=" N ILE C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 375 removed outlier: 3.584A pdb=" N LEU C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 420 removed outlier: 4.163A pdb=" N VAL C 396 " --> pdb=" O PRO C 392 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP C 397 " --> pdb=" O GLN C 393 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA C 398 " --> pdb=" O ARG C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 437 Processing helix chain 'C' and resid 453 through 469 Processing helix chain 'C' and resid 470 through 473 Processing helix chain 'C' and resid 474 through 479 removed outlier: 4.277A pdb=" N LEU C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 474 through 479' Processing helix chain 'D' and resid 2 through 20 removed outlier: 3.727A pdb=" N ILE D 6 " --> pdb=" O GLN D 2 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG D 8 " --> pdb=" O ARG D 4 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.673A pdb=" N LEU D 26 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 55 Processing helix chain 'D' and resid 69 through 82 Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.682A pdb=" N PHE D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 89 " --> pdb=" O LEU D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 97 through 109 Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 124 through 143 removed outlier: 3.713A pdb=" N ILE D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 202 removed outlier: 4.493A pdb=" N ALA D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 217 Processing helix chain 'D' and resid 235 through 251 removed outlier: 3.600A pdb=" N ALA D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 removed outlier: 4.034A pdb=" N ALA D 258 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.585A pdb=" N TYR D 270 " --> pdb=" O PRO D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 298 Processing helix chain 'D' and resid 302 through 319 removed outlier: 3.561A pdb=" N ALA D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.731A pdb=" N ILE D 345 " --> pdb=" O PHE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 377 Processing helix chain 'D' and resid 392 through 420 removed outlier: 4.110A pdb=" N VAL D 396 " --> pdb=" O PRO D 392 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP D 397 " --> pdb=" O GLN D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.572A pdb=" N ALA D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 469 Processing helix chain 'D' and resid 471 through 479 removed outlier: 4.201A pdb=" N LEU D 475 " --> pdb=" O ILE D 471 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 477 " --> pdb=" O THR D 473 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 54 through 61 Processing helix chain 'E' and resid 75 through 91 Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 107 through 112 Processing helix chain 'E' and resid 241 through 252 Processing helix chain 'E' and resid 264 through 271 removed outlier: 3.906A pdb=" N LYS E 269 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.879A pdb=" N LEU E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 298 removed outlier: 3.668A pdb=" N VAL E 298 " --> pdb=" O ILE E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 322 removed outlier: 3.833A pdb=" N ASN E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 334 No H-bonds generated for 'chain 'E' and resid 332 through 334' Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'F' and resid 9 through 20 Processing helix chain 'F' and resid 54 through 61 Processing helix chain 'F' and resid 75 through 91 Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 107 through 112 Processing helix chain 'F' and resid 243 through 252 Processing helix chain 'F' and resid 264 through 274 Processing helix chain 'F' and resid 286 through 291 removed outlier: 4.286A pdb=" N LEU F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 298 removed outlier: 3.711A pdb=" N VAL F 298 " --> pdb=" O ILE F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 321 Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 349 through 360 removed outlier: 4.359A pdb=" N ALA F 353 " --> pdb=" O SER F 349 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR F 354 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 20 Processing helix chain 'G' and resid 54 through 61 Processing helix chain 'G' and resid 75 through 91 Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 107 through 112 Processing helix chain 'G' and resid 241 through 252 Processing helix chain 'G' and resid 264 through 274 Processing helix chain 'G' and resid 286 through 291 removed outlier: 4.307A pdb=" N LEU G 290 " --> pdb=" O ASP G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 298 removed outlier: 3.722A pdb=" N VAL G 298 " --> pdb=" O ILE G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 321 Processing helix chain 'G' and resid 335 through 340 Processing helix chain 'G' and resid 350 through 355 Processing helix chain 'G' and resid 355 through 360 Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 54 through 61 Processing helix chain 'H' and resid 75 through 91 Processing helix chain 'H' and resid 101 through 106 Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 243 through 252 Processing helix chain 'H' and resid 264 through 274 Processing helix chain 'H' and resid 286 through 291 removed outlier: 4.277A pdb=" N LEU H 290 " --> pdb=" O ASP H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 298 removed outlier: 3.746A pdb=" N VAL H 298 " --> pdb=" O ILE H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 321 Processing helix chain 'H' and resid 335 through 340 Processing helix chain 'H' and resid 350 through 355 Processing helix chain 'H' and resid 355 through 360 Processing sheet with id=AA1, first strand: chain 'E' and resid 48 through 49 removed outlier: 8.139A pdb=" N VAL E 48 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE E 28 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 278 through 281 removed outlier: 6.382A pdb=" N PHE E 301 " --> pdb=" O MET E 327 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU E 329 " --> pdb=" O PHE E 301 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ALA E 303 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE E 348 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL E 328 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 48 through 49 removed outlier: 8.139A pdb=" N VAL F 48 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE F 28 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 278 through 281 removed outlier: 5.933A pdb=" N VAL F 257 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE F 280 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU F 259 " --> pdb=" O PHE F 280 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE F 301 " --> pdb=" O MET F 327 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU F 329 " --> pdb=" O PHE F 301 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA F 303 " --> pdb=" O LEU F 329 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL F 326 " --> pdb=" O VAL F 346 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE F 348 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL F 328 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 48 through 49 removed outlier: 8.139A pdb=" N VAL G 48 " --> pdb=" O ILE G 26 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE G 28 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 278 through 281 removed outlier: 5.966A pdb=" N VAL G 257 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE G 280 " --> pdb=" O VAL G 257 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU G 259 " --> pdb=" O PHE G 280 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE G 348 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL G 328 " --> pdb=" O ILE G 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 48 through 49 removed outlier: 8.139A pdb=" N VAL H 48 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE H 28 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS H 2 " --> pdb=" O MET H 68 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL H 70 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE H 4 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU H 69 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 278 through 281 removed outlier: 5.826A pdb=" N VAL H 257 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE H 280 " --> pdb=" O VAL H 257 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU H 259 " --> pdb=" O PHE H 280 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE H 348 " --> pdb=" O VAL H 326 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL H 328 " --> pdb=" O ILE H 348 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3270 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: 5.94 Time building geometry restraints manager: 7.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.71 - 0.94: 1 0.94 - 1.17: 1 1.17 - 1.40: 8552 1.40 - 1.63: 12350 1.63 - 1.86: 174 Bond restraints: 21078 Sorted by residual: bond pdb=" C LEU E 69 " pdb=" N VAL E 70 " ideal model delta sigma weight residual 1.332 0.705 0.627 1.23e-02 6.61e+03 2.60e+03 bond pdb=" C MET E 68 " pdb=" N LEU E 69 " ideal model delta sigma weight residual 1.329 1.567 -0.238 1.40e-02 5.10e+03 2.88e+02 bond pdb=" C ASN E 18 " pdb=" N LEU E 19 " ideal model delta sigma weight residual 1.333 1.130 0.203 1.43e-02 4.89e+03 2.02e+02 bond pdb=" C LEU E 19 " pdb=" N VAL E 20 " ideal model delta sigma weight residual 1.332 1.488 -0.156 1.36e-02 5.41e+03 1.31e+02 bond pdb=" CA SER F 314 " pdb=" C SER F 314 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.29e-02 6.01e+03 1.09e+01 ... (remaining 21073 not shown) Histogram of bond angle deviations from ideal: 77.04 - 94.22: 2 94.22 - 111.41: 8531 111.41 - 128.59: 19911 128.59 - 145.78: 205 145.78 - 162.96: 2 Bond angle restraints: 28651 Sorted by residual: angle pdb=" O MET E 68 " pdb=" C MET E 68 " pdb=" N LEU E 69 " ideal model delta sigma weight residual 123.25 77.04 46.21 1.14e+00 7.69e-01 1.64e+03 angle pdb=" CA MET E 68 " pdb=" C MET E 68 " pdb=" N LEU E 69 " ideal model delta sigma weight residual 115.36 161.19 -45.83 1.48e+00 4.57e-01 9.59e+02 angle pdb=" C MET E 68 " pdb=" N LEU E 69 " pdb=" CA LEU E 69 " ideal model delta sigma weight residual 121.70 162.96 -41.26 1.80e+00 3.09e-01 5.25e+02 angle pdb=" C ASN E 18 " pdb=" N LEU E 19 " pdb=" CA LEU E 19 " ideal model delta sigma weight residual 121.92 86.82 35.10 1.73e+00 3.34e-01 4.12e+02 angle pdb=" CA ASN E 18 " pdb=" C ASN E 18 " pdb=" N LEU E 19 " ideal model delta sigma weight residual 118.17 96.79 21.38 1.33e+00 5.65e-01 2.58e+02 ... (remaining 28646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 11046 16.74 - 33.48: 951 33.48 - 50.22: 165 50.22 - 66.96: 32 66.96 - 83.69: 18 Dihedral angle restraints: 12212 sinusoidal: 4518 harmonic: 7694 Sorted by residual: dihedral pdb=" CA CYS C 251 " pdb=" C CYS C 251 " pdb=" N ASN C 252 " pdb=" CA ASN C 252 " ideal model delta harmonic sigma weight residual 180.00 -96.39 -83.61 0 5.00e+00 4.00e-02 2.80e+02 dihedral pdb=" CA GLU B 275 " pdb=" C GLU B 275 " pdb=" N PHE B 276 " pdb=" CA PHE B 276 " ideal model delta harmonic sigma weight residual 180.00 -130.51 -49.49 0 5.00e+00 4.00e-02 9.80e+01 dihedral pdb=" CA VAL C 118 " pdb=" C VAL C 118 " pdb=" N GLY C 119 " pdb=" CA GLY C 119 " ideal model delta harmonic sigma weight residual -180.00 -139.24 -40.76 0 5.00e+00 4.00e-02 6.65e+01 ... (remaining 12209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2930 0.123 - 0.246: 424 0.246 - 0.369: 70 0.369 - 0.492: 11 0.492 - 0.615: 6 Chirality restraints: 3441 Sorted by residual: chirality pdb=" CB VAL D 445 " pdb=" CA VAL D 445 " pdb=" CG1 VAL D 445 " pdb=" CG2 VAL D 445 " both_signs ideal model delta sigma weight residual False -2.63 -2.01 -0.62 2.00e-01 2.50e+01 9.47e+00 chirality pdb=" CB ILE B 220 " pdb=" CA ILE B 220 " pdb=" CG1 ILE B 220 " pdb=" CG2 ILE B 220 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.68e+00 chirality pdb=" CA ASP H 308 " pdb=" N ASP H 308 " pdb=" C ASP H 308 " pdb=" CB ASP H 308 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.90e+00 ... (remaining 3438 not shown) Planarity restraints: 3553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 55 " -0.102 5.00e-02 4.00e+02 1.49e-01 3.53e+01 pdb=" N PRO B 56 " 0.257 5.00e-02 4.00e+02 pdb=" CA PRO B 56 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO B 56 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 19 " -0.035 2.00e-02 2.50e+03 5.89e-02 3.47e+01 pdb=" C LEU E 19 " 0.102 2.00e-02 2.50e+03 pdb=" O LEU E 19 " -0.034 2.00e-02 2.50e+03 pdb=" N VAL E 20 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 466 " -0.026 2.00e-02 2.50e+03 5.15e-02 2.66e+01 pdb=" C PHE C 466 " 0.089 2.00e-02 2.50e+03 pdb=" O PHE C 466 " -0.033 2.00e-02 2.50e+03 pdb=" N GLY C 467 " -0.030 2.00e-02 2.50e+03 ... (remaining 3550 not shown) Histogram of nonbonded interaction distances: 0.24 - 1.18: 11 1.18 - 2.11: 78 2.11 - 3.04: 12770 3.04 - 3.97: 52828 3.97 - 4.90: 91129 Warning: very small nonbonded interaction distances. Nonbonded interactions: 156816 Sorted by model distance: nonbonded pdb=" CD GLU F 77 " pdb=" CD GLU H 77 " model vdw 0.244 3.500 nonbonded pdb=" SD MET F 68 " pdb=" CG LEU F 358 " model vdw 1.061 3.830 nonbonded pdb=" OE2 GLU F 107 " pdb=" CE1 HIS H 54 " model vdw 1.082 3.260 nonbonded pdb=" CE1 HIS F 54 " pdb=" OE2 GLU H 107 " model vdw 1.090 3.260 nonbonded pdb=" OD1 ASP G 308 " pdb=" NE2 GLN G 331 " model vdw 1.096 2.520 ... (remaining 156811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 28 or resid 37 through 89 or resid 94 through 11 \ 7 or resid 124 through 153 or resid 178 through 267 or (resid 268 and (name N or \ name CA or name C or name O or name CB )) or resid 269 through 270 or resid 275 \ through 483)) selection = (chain 'B' and (resid 1 through 28 or resid 37 through 61 or resid 68 through 11 \ 7 or resid 124 through 267 or (resid 268 and (name N or name CA or name C or nam \ e O or name CB )) or resid 269 through 483)) selection = (chain 'C' and (resid 1 through 28 or resid 37 through 89 or resid 94 through 11 \ 7 or resid 124 through 270 or resid 275 through 483)) selection = (chain 'D' and (resid 1 through 28 or resid 37 through 89 or resid 94 through 11 \ 7 or resid 124 through 267 or (resid 268 and (name N or name CA or name C or nam \ e O or name CB )) or resid 269 through 270 or resid 275 through 483)) } ncs_group { reference = (chain 'E' and (resid 1 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 360)) selection = (chain 'F' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 67 or (resid 68 and (name N or name \ CA or name C or name O or name CB )) or resid 69 through 76 or (resid 77 and (n \ ame N or name CA or name C or name O or name CB )) or resid 78 through 308 or (r \ esid 309 and (name N or name CA or name C or name O or name CB )) or resid 310 t \ hrough 331 or (resid 332 and (name N or name CA or name C or name O or name CB ) \ ) or resid 333 through 357 or (resid 358 and (name N or name CA or name C or nam \ e O or name CB )) or resid 359 through 360)) selection = (chain 'G' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 331 or (resid 332 and (name N or na \ me CA or name C or name O or name CB )) or resid 333 through 360)) selection = (chain 'H' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 76 or (resid 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 308 or (resid 309 and \ (name N or name CA or name C or name O or name CB )) or resid 310 through 331 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 3 through 360)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 3.550 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 49.300 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4896 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 : 0.010 0.627 21078 Z= 0.661 Angle : 1.790 46.214 28651 Z= 1.029 Chirality : 0.094 0.615 3441 Planarity : 0.011 0.149 3553 Dihedral : 13.199 83.694 7226 Min Nonbonded Distance : 0.244 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.00 % Favored : 95.65 % Rotamer: Outliers : 5.36 % Allowed : 10.55 % Favored : 84.09 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.54 (0.15), residues: 2623 helix: 0.95 (0.13), residues: 1393 sheet: -0.70 (0.41), residues: 180 loop : -2.17 (0.16), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.005 TRP B 400 HIS 0.022 0.003 HIS D 448 PHE 0.070 0.005 PHE B 323 TYR 0.029 0.003 TYR A 304 ARG 0.012 0.001 ARG C 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 596 time to evaluate : 2.172 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: A 8 ARG cc_start: 0.6290 (ttp80) cc_final: 0.5987 (ttp-170) REVERT: A 21 MET cc_start: 0.6115 (mmt) cc_final: 0.5888 (mmm) REVERT: A 79 VAL cc_start: 0.5977 (OUTLIER) cc_final: 0.5691 (t) REVERT: A 143 ILE cc_start: 0.6518 (pt) cc_final: 0.6315 (tt) REVERT: A 200 PHE cc_start: 0.6002 (m-10) cc_final: 0.5529 (m-80) REVERT: A 270 TYR cc_start: 0.7170 (m-10) cc_final: 0.6822 (m-80) REVERT: A 280 ILE cc_start: 0.7403 (mm) cc_final: 0.7195 (mp) REVERT: A 293 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6733 (tm) REVERT: A 311 LEU cc_start: 0.6454 (tm) cc_final: 0.6162 (mm) REVERT: A 331 TRP cc_start: 0.7039 (m100) cc_final: 0.6690 (m100) REVERT: A 339 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7531 (mp) REVERT: A 343 SER cc_start: 0.7404 (p) cc_final: 0.6988 (m) REVERT: A 345 ILE cc_start: 0.6880 (mt) cc_final: 0.6631 (tp) REVERT: A 356 MET cc_start: 0.7967 (ptp) cc_final: 0.7734 (ptm) REVERT: A 359 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7083 (tt) REVERT: A 370 ARG cc_start: 0.6663 (ttt180) cc_final: 0.6281 (mmt-90) REVERT: A 385 LYS cc_start: 0.7044 (ptpt) cc_final: 0.6387 (ptmm) REVERT: A 447 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5405 (mm) REVERT: A 460 LEU cc_start: 0.7262 (mt) cc_final: 0.7001 (mm) REVERT: A 470 GLU cc_start: 0.5591 (OUTLIER) cc_final: 0.5127 (tp30) REVERT: A 477 LEU cc_start: 0.7581 (mm) cc_final: 0.7159 (mt) REVERT: B 21 MET cc_start: 0.6383 (mmt) cc_final: 0.6139 (mmm) REVERT: B 60 HIS cc_start: 0.5192 (t70) cc_final: 0.4927 (t70) REVERT: B 103 PHE cc_start: 0.6899 (t80) cc_final: 0.6698 (t80) REVERT: B 104 GLU cc_start: 0.7428 (tp30) cc_final: 0.6985 (tp30) REVERT: B 153 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7037 (pp) REVERT: B 188 ILE cc_start: 0.7159 (mm) cc_final: 0.6864 (pt) REVERT: B 190 LEU cc_start: 0.7141 (tm) cc_final: 0.6758 (tp) REVERT: B 201 TRP cc_start: 0.6640 (t60) cc_final: 0.6092 (t60) REVERT: B 207 PRO cc_start: 0.7307 (Cg_exo) cc_final: 0.7089 (Cg_endo) REVERT: B 211 ILE cc_start: 0.6398 (mt) cc_final: 0.6114 (pp) REVERT: B 236 TYR cc_start: 0.7403 (m-80) cc_final: 0.7052 (m-80) REVERT: B 311 LEU cc_start: 0.6419 (tm) cc_final: 0.6150 (mm) REVERT: B 334 PHE cc_start: 0.6288 (t80) cc_final: 0.5677 (t80) REVERT: B 339 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7385 (mp) REVERT: B 343 SER cc_start: 0.6826 (p) cc_final: 0.6491 (m) REVERT: B 370 ARG cc_start: 0.6297 (ttt180) cc_final: 0.5895 (mmm160) REVERT: B 373 LYS cc_start: 0.7100 (mtpp) cc_final: 0.6275 (mtpp) REVERT: B 382 TYR cc_start: 0.5072 (m-80) cc_final: 0.4239 (m-80) REVERT: B 391 LEU cc_start: 0.7644 (pp) cc_final: 0.7089 (tp) REVERT: B 397 ASP cc_start: 0.7028 (m-30) cc_final: 0.6770 (m-30) REVERT: B 466 PHE cc_start: 0.6429 (m-10) cc_final: 0.6217 (m-80) REVERT: B 477 LEU cc_start: 0.6686 (mm) cc_final: 0.6383 (mp) REVERT: C 70 PHE cc_start: 0.6342 (m-80) cc_final: 0.6128 (m-10) REVERT: C 74 VAL cc_start: 0.6467 (t) cc_final: 0.6261 (m) REVERT: C 130 TYR cc_start: 0.5788 (t80) cc_final: 0.5568 (t80) REVERT: C 143 ILE cc_start: 0.7303 (pt) cc_final: 0.6601 (tp) REVERT: C 190 LEU cc_start: 0.6906 (tm) cc_final: 0.6577 (tp) REVERT: C 270 TYR cc_start: 0.7021 (m-10) cc_final: 0.6774 (m-80) REVERT: C 292 LEU cc_start: 0.6946 (mt) cc_final: 0.6739 (mt) REVERT: C 311 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6115 (mm) REVERT: C 331 TRP cc_start: 0.6906 (m100) cc_final: 0.6222 (m-90) REVERT: C 339 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7573 (mp) REVERT: C 345 ILE cc_start: 0.6641 (mt) cc_final: 0.6416 (tp) REVERT: C 356 MET cc_start: 0.7676 (ptp) cc_final: 0.7267 (ptm) REVERT: C 373 LYS cc_start: 0.7328 (mtpp) cc_final: 0.6757 (mtpp) REVERT: C 382 TYR cc_start: 0.5061 (m-80) cc_final: 0.4572 (m-80) REVERT: C 385 LYS cc_start: 0.6865 (ptpt) cc_final: 0.6401 (pttm) REVERT: C 392 PRO cc_start: 0.7508 (Cg_endo) cc_final: 0.7180 (Cg_exo) REVERT: D 8 ARG cc_start: 0.6643 (ttp80) cc_final: 0.6321 (ttp-170) REVERT: D 21 MET cc_start: 0.6238 (mmt) cc_final: 0.5549 (mmm) REVERT: D 189 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.6423 (t80) REVERT: D 190 LEU cc_start: 0.7159 (tm) cc_final: 0.6776 (tp) REVERT: D 280 ILE cc_start: 0.7718 (mm) cc_final: 0.7471 (mp) REVERT: D 311 LEU cc_start: 0.6245 (tm) cc_final: 0.5933 (mm) REVERT: D 312 PHE cc_start: 0.6016 (t80) cc_final: 0.5777 (t80) REVERT: D 331 TRP cc_start: 0.6739 (m100) cc_final: 0.6136 (m-90) REVERT: D 339 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7594 (mp) REVERT: D 356 MET cc_start: 0.8125 (ptp) cc_final: 0.7685 (ptm) REVERT: D 358 VAL cc_start: 0.7102 (t) cc_final: 0.6656 (p) REVERT: D 359 ILE cc_start: 0.7535 (pp) cc_final: 0.7139 (pt) REVERT: D 361 ILE cc_start: 0.6497 (mm) cc_final: 0.6195 (tt) REVERT: D 362 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6227 (mp) REVERT: D 370 ARG cc_start: 0.6501 (ttt180) cc_final: 0.5373 (ptt180) REVERT: D 373 LYS cc_start: 0.7381 (mtpp) cc_final: 0.6646 (mtpp) REVERT: D 382 TYR cc_start: 0.5187 (m-80) cc_final: 0.4228 (m-80) REVERT: D 385 LYS cc_start: 0.6786 (ptpt) cc_final: 0.6506 (ptmm) REVERT: D 423 ASP cc_start: 0.6563 (p0) cc_final: 0.6303 (p0) REVERT: D 476 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7676 (pt) REVERT: D 477 LEU cc_start: 0.7270 (mm) cc_final: 0.6982 (tp) REVERT: E 242 ASN cc_start: 0.7148 (m110) cc_final: 0.6896 (m-40) REVERT: E 259 LEU cc_start: 0.5080 (tt) cc_final: 0.4752 (tm) REVERT: E 260 ILE cc_start: 0.6103 (mt) cc_final: 0.5471 (mm) REVERT: E 293 GLU cc_start: 0.5473 (OUTLIER) cc_final: 0.5139 (mp0) REVERT: E 301 PHE cc_start: 0.6468 (t80) cc_final: 0.6205 (t80) REVERT: E 308 ASP cc_start: 0.3976 (OUTLIER) cc_final: 0.3696 (p0) REVERT: E 309 GLU cc_start: 0.4449 (OUTLIER) cc_final: 0.3639 (pm20) REVERT: F 1 MET cc_start: -0.0126 (tpp) cc_final: -0.0349 (mmm) REVERT: F 259 LEU cc_start: 0.5293 (tt) cc_final: 0.4854 (tm) REVERT: F 260 ILE cc_start: 0.6101 (mt) cc_final: 0.5437 (mm) REVERT: F 294 ASN cc_start: 0.6897 (m-40) cc_final: 0.6580 (m-40) REVERT: F 309 GLU cc_start: 0.3230 (OUTLIER) cc_final: 0.2980 (pp20) REVERT: F 325 LYS cc_start: 0.6021 (tttt) cc_final: 0.5425 (mppt) REVERT: F 328 VAL cc_start: 0.6916 (t) cc_final: 0.6562 (p) REVERT: F 348 ILE cc_start: 0.6957 (mp) cc_final: 0.6602 (pt) REVERT: G 238 VAL cc_start: 0.6418 (m) cc_final: 0.6178 (p) REVERT: G 259 LEU cc_start: 0.5536 (tt) cc_final: 0.5215 (tm) REVERT: G 275 GLU cc_start: 0.4800 (tp30) cc_final: 0.4371 (tp30) REVERT: G 294 ASN cc_start: 0.6772 (m-40) cc_final: 0.6505 (m-40) REVERT: G 313 MET cc_start: 0.5254 (mmm) cc_final: 0.4947 (mmm) REVERT: H 246 SER cc_start: 0.7747 (t) cc_final: 0.7290 (m) REVERT: H 279 VAL cc_start: 0.4304 (OUTLIER) cc_final: 0.3720 (p) REVERT: H 294 ASN cc_start: 0.6848 (m-40) cc_final: 0.6550 (m-40) REVERT: H 313 MET cc_start: 0.5283 (mmm) cc_final: 0.4975 (mmm) outliers start: 117 outliers final: 40 residues processed: 691 average time/residue: 0.7074 time to fit residues: 600.3289 Evaluate side-chains 485 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 426 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 476 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 293 GLU Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 302 ILE Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 305 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 241 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 436 ASN A 448 HIS A 453 ASN B 57 ASN B 60 HIS ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 266 HIS B 367 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 HIS ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 HIS C 448 HIS C 453 ASN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 HIS F 311 ASN G 91 ASN G 121 HIS H 91 ASN ** H 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4872 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21078 Z= 0.192 Angle : 0.766 16.449 28651 Z= 0.377 Chirality : 0.046 0.323 3441 Planarity : 0.005 0.081 3553 Dihedral : 8.031 103.016 2907 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.10 % Rotamer: Outliers : 5.91 % Allowed : 15.68 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 2623 helix: 0.11 (0.13), residues: 1366 sheet: -0.22 (0.37), residues: 200 loop : -1.83 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 400 HIS 0.004 0.001 HIS D 448 PHE 0.028 0.002 PHE B 291 TYR 0.023 0.002 TYR E 104 ARG 0.004 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 477 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6328 (mmt) cc_final: 0.5887 (mmm) REVERT: A 45 VAL cc_start: 0.5981 (p) cc_final: 0.5631 (m) REVERT: A 104 GLU cc_start: 0.6833 (tp30) cc_final: 0.6564 (tp30) REVERT: A 107 SER cc_start: 0.5956 (OUTLIER) cc_final: 0.5702 (p) REVERT: A 143 ILE cc_start: 0.7202 (pt) cc_final: 0.6830 (tp) REVERT: A 181 THR cc_start: 0.7443 (m) cc_final: 0.7231 (p) REVERT: A 190 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6770 (tp) REVERT: A 280 ILE cc_start: 0.7476 (mm) cc_final: 0.7201 (mp) REVERT: A 286 LEU cc_start: 0.6937 (tt) cc_final: 0.6464 (mt) REVERT: A 311 LEU cc_start: 0.6485 (tm) cc_final: 0.6257 (mm) REVERT: A 339 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7274 (mp) REVERT: A 343 SER cc_start: 0.7263 (p) cc_final: 0.6651 (m) REVERT: A 370 ARG cc_start: 0.6177 (ttt180) cc_final: 0.5787 (mmm160) REVERT: A 373 LYS cc_start: 0.6683 (tttt) cc_final: 0.6394 (tttt) REVERT: A 382 TYR cc_start: 0.4783 (m-80) cc_final: 0.4054 (m-80) REVERT: A 385 LYS cc_start: 0.6717 (ptpt) cc_final: 0.6157 (pttm) REVERT: A 391 LEU cc_start: 0.7364 (mt) cc_final: 0.7087 (mm) REVERT: A 395 VAL cc_start: 0.7670 (OUTLIER) cc_final: 0.7358 (p) REVERT: A 423 ASP cc_start: 0.7094 (p0) cc_final: 0.6891 (p0) REVERT: A 447 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5433 (mm) REVERT: A 470 GLU cc_start: 0.5754 (OUTLIER) cc_final: 0.5329 (tp30) REVERT: A 477 LEU cc_start: 0.7385 (mm) cc_final: 0.6844 (mt) REVERT: B 54 TRP cc_start: 0.7041 (t-100) cc_final: 0.6806 (t-100) REVERT: B 103 PHE cc_start: 0.6894 (t80) cc_final: 0.6631 (t80) REVERT: B 104 GLU cc_start: 0.7039 (tp30) cc_final: 0.6827 (tp30) REVERT: B 188 ILE cc_start: 0.7372 (mm) cc_final: 0.6952 (pt) REVERT: B 190 LEU cc_start: 0.7252 (tm) cc_final: 0.6863 (tp) REVERT: B 201 TRP cc_start: 0.6667 (t60) cc_final: 0.6187 (t60) REVERT: B 236 TYR cc_start: 0.7192 (m-80) cc_final: 0.6974 (m-80) REVERT: B 238 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7119 (mm) REVERT: B 277 ARG cc_start: 0.4733 (ptp90) cc_final: 0.3870 (ptp90) REVERT: B 288 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6340 (tp) REVERT: B 311 LEU cc_start: 0.6434 (tm) cc_final: 0.6218 (mm) REVERT: B 312 PHE cc_start: 0.6104 (t80) cc_final: 0.5895 (t80) REVERT: B 370 ARG cc_start: 0.5903 (ttt180) cc_final: 0.5691 (ptm160) REVERT: B 373 LYS cc_start: 0.6612 (mtpp) cc_final: 0.6306 (tttp) REVERT: B 379 ARG cc_start: 0.6916 (ttm170) cc_final: 0.6687 (ttm170) REVERT: B 382 TYR cc_start: 0.5013 (m-80) cc_final: 0.4329 (m-80) REVERT: B 391 LEU cc_start: 0.7648 (pp) cc_final: 0.6865 (mm) REVERT: B 457 LYS cc_start: 0.7574 (mttm) cc_final: 0.7298 (mttp) REVERT: B 477 LEU cc_start: 0.6830 (mm) cc_final: 0.6547 (mt) REVERT: C 190 LEU cc_start: 0.7095 (tm) cc_final: 0.6769 (tp) REVERT: C 271 TRP cc_start: 0.7294 (t-100) cc_final: 0.6768 (t-100) REVERT: C 356 MET cc_start: 0.7833 (ptp) cc_final: 0.7363 (ptm) REVERT: C 363 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6454 (tt) REVERT: C 370 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.5908 (mmt180) REVERT: C 373 LYS cc_start: 0.6587 (mtpp) cc_final: 0.6103 (mtpp) REVERT: C 382 TYR cc_start: 0.5113 (m-80) cc_final: 0.4616 (m-80) REVERT: C 392 PRO cc_start: 0.7500 (Cg_endo) cc_final: 0.7069 (Cg_exo) REVERT: C 395 VAL cc_start: 0.7486 (t) cc_final: 0.7123 (m) REVERT: C 457 LYS cc_start: 0.7815 (mttt) cc_final: 0.7585 (mttt) REVERT: D 8 ARG cc_start: 0.6367 (ttp80) cc_final: 0.6074 (ttp-110) REVERT: D 21 MET cc_start: 0.6441 (mmt) cc_final: 0.6070 (mmm) REVERT: D 54 TRP cc_start: 0.7189 (t-100) cc_final: 0.6947 (t-100) REVERT: D 102 PHE cc_start: 0.6215 (m-80) cc_final: 0.5954 (m-80) REVERT: D 107 SER cc_start: 0.5631 (OUTLIER) cc_final: 0.5415 (p) REVERT: D 190 LEU cc_start: 0.7064 (tm) cc_final: 0.6672 (tp) REVERT: D 202 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5662 (tp) REVERT: D 280 ILE cc_start: 0.7513 (mm) cc_final: 0.7271 (OUTLIER) REVERT: D 286 LEU cc_start: 0.6852 (tt) cc_final: 0.6519 (mt) REVERT: D 312 PHE cc_start: 0.6013 (t80) cc_final: 0.5758 (t80) REVERT: D 358 VAL cc_start: 0.6814 (t) cc_final: 0.6401 (p) REVERT: D 361 ILE cc_start: 0.6233 (mm) cc_final: 0.5903 (tt) REVERT: D 362 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.5827 (mt) REVERT: D 370 ARG cc_start: 0.6093 (ttt180) cc_final: 0.5727 (mmp80) REVERT: D 373 LYS cc_start: 0.6932 (mtpp) cc_final: 0.6642 (tttp) REVERT: D 382 TYR cc_start: 0.4978 (m-80) cc_final: 0.3845 (m-80) REVERT: D 423 ASP cc_start: 0.7008 (p0) cc_final: 0.6608 (p0) REVERT: D 477 LEU cc_start: 0.7446 (mm) cc_final: 0.7246 (tp) REVERT: E 236 MET cc_start: 0.3780 (OUTLIER) cc_final: 0.2949 (tpp) REVERT: E 242 ASN cc_start: 0.7003 (m110) cc_final: 0.6784 (m-40) REVERT: E 286 ASP cc_start: 0.1884 (OUTLIER) cc_final: 0.0620 (m-30) REVERT: E 288 GLU cc_start: 0.2915 (OUTLIER) cc_final: 0.1745 (pm20) REVERT: E 301 PHE cc_start: 0.6475 (t80) cc_final: 0.6125 (t80) REVERT: E 321 MET cc_start: 0.4492 (mmt) cc_final: 0.4105 (mmp) REVERT: E 327 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.6227 (mpp) REVERT: F 68 MET cc_start: 0.2448 (ttm) cc_final: 0.1781 (tpp) REVERT: F 238 VAL cc_start: 0.5700 (OUTLIER) cc_final: 0.5238 (p) REVERT: F 325 LYS cc_start: 0.5618 (tttt) cc_final: 0.5337 (mppt) REVERT: G 236 MET cc_start: 0.4027 (mtp) cc_final: 0.3281 (tpp) REVERT: G 238 VAL cc_start: 0.6207 (m) cc_final: 0.5949 (p) REVERT: G 247 LEU cc_start: 0.6764 (tp) cc_final: 0.6249 (pp) REVERT: G 313 MET cc_start: 0.5184 (mmm) cc_final: 0.4830 (mmm) REVERT: G 327 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.5703 (tmt) REVERT: H 246 SER cc_start: 0.7771 (t) cc_final: 0.7216 (m) REVERT: H 259 LEU cc_start: 0.5166 (tp) cc_final: 0.4868 (tm) REVERT: H 313 MET cc_start: 0.5156 (mmm) cc_final: 0.4847 (mmm) outliers start: 129 outliers final: 51 residues processed: 564 average time/residue: 0.7933 time to fit residues: 539.4304 Evaluate side-chains 483 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 414 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 370 ARG Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 294 ASN Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain F residue 236 MET Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 305 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 0.0170 chunk 201 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 241 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 239 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 313 GLN B 57 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 313 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS D 437 ASN D 453 ASN E 91 ASN E 311 ASN F 91 ASN G 18 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4856 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21078 Z= 0.164 Angle : 0.661 12.808 28651 Z= 0.323 Chirality : 0.043 0.368 3441 Planarity : 0.004 0.072 3553 Dihedral : 6.329 59.035 2853 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.78 % Allowed : 16.96 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 2623 helix: 0.07 (0.13), residues: 1368 sheet: 0.58 (0.43), residues: 156 loop : -1.80 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 400 HIS 0.003 0.001 HIS A 448 PHE 0.024 0.001 PHE D 334 TYR 0.032 0.001 TYR B 304 ARG 0.003 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 446 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6405 (mmt) cc_final: 0.5859 (mmm) REVERT: A 103 PHE cc_start: 0.6588 (t80) cc_final: 0.6329 (t80) REVERT: A 107 SER cc_start: 0.5776 (t) cc_final: 0.5572 (p) REVERT: A 143 ILE cc_start: 0.7094 (pt) cc_final: 0.6583 (tp) REVERT: A 280 ILE cc_start: 0.7499 (mm) cc_final: 0.7209 (mp) REVERT: A 285 LEU cc_start: 0.7053 (tt) cc_final: 0.6842 (tp) REVERT: A 286 LEU cc_start: 0.6787 (tt) cc_final: 0.6539 (mt) REVERT: A 311 LEU cc_start: 0.6469 (tm) cc_final: 0.6224 (mm) REVERT: A 343 SER cc_start: 0.7200 (p) cc_final: 0.6986 (t) REVERT: A 361 ILE cc_start: 0.6028 (mt) cc_final: 0.5491 (tt) REVERT: A 385 LYS cc_start: 0.6684 (ptpt) cc_final: 0.6074 (pttm) REVERT: A 391 LEU cc_start: 0.7220 (mt) cc_final: 0.6953 (mm) REVERT: A 423 ASP cc_start: 0.7162 (p0) cc_final: 0.6924 (p0) REVERT: A 447 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5457 (mm) REVERT: A 454 ASP cc_start: 0.6622 (m-30) cc_final: 0.6259 (p0) REVERT: A 477 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6829 (mt) REVERT: B 21 MET cc_start: 0.6799 (mmp) cc_final: 0.6069 (mmm) REVERT: B 54 TRP cc_start: 0.6858 (t-100) cc_final: 0.6638 (t-100) REVERT: B 188 ILE cc_start: 0.7334 (mm) cc_final: 0.6925 (pt) REVERT: B 190 LEU cc_start: 0.7088 (tm) cc_final: 0.6718 (tp) REVERT: B 201 TRP cc_start: 0.6599 (t60) cc_final: 0.6274 (t60) REVERT: B 277 ARG cc_start: 0.4343 (ptp90) cc_final: 0.3537 (ttt-90) REVERT: B 288 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6394 (tp) REVERT: B 373 LYS cc_start: 0.6623 (mtpp) cc_final: 0.6399 (tttp) REVERT: B 382 TYR cc_start: 0.4737 (m-80) cc_final: 0.3818 (m-80) REVERT: B 391 LEU cc_start: 0.7433 (pp) cc_final: 0.6750 (mm) REVERT: B 453 ASN cc_start: 0.6920 (t0) cc_final: 0.6605 (t0) REVERT: B 477 LEU cc_start: 0.6924 (mm) cc_final: 0.6636 (mt) REVERT: C 190 LEU cc_start: 0.7027 (tm) cc_final: 0.6691 (tp) REVERT: C 271 TRP cc_start: 0.7346 (t-100) cc_final: 0.6847 (t-100) REVERT: C 356 MET cc_start: 0.7892 (ptp) cc_final: 0.7438 (ptm) REVERT: C 363 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6567 (tt) REVERT: C 373 LYS cc_start: 0.6504 (mtpp) cc_final: 0.6062 (mtpp) REVERT: C 382 TYR cc_start: 0.4964 (m-80) cc_final: 0.2557 (m-80) REVERT: C 457 LYS cc_start: 0.7766 (mttt) cc_final: 0.7450 (mttt) REVERT: C 469 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6113 (pt) REVERT: D 8 ARG cc_start: 0.6312 (ttp80) cc_final: 0.6079 (ttp-110) REVERT: D 21 MET cc_start: 0.6480 (mmt) cc_final: 0.5630 (mmm) REVERT: D 54 TRP cc_start: 0.7042 (t-100) cc_final: 0.6779 (t-100) REVERT: D 190 LEU cc_start: 0.6971 (tm) cc_final: 0.6558 (tp) REVERT: D 202 LEU cc_start: 0.5704 (OUTLIER) cc_final: 0.5398 (tp) REVERT: D 275 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.6236 (tt0) REVERT: D 280 ILE cc_start: 0.7477 (mm) cc_final: 0.7269 (OUTLIER) REVERT: D 288 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6326 (tp) REVERT: D 304 TYR cc_start: 0.5971 (m-10) cc_final: 0.5501 (m-80) REVERT: D 312 PHE cc_start: 0.5792 (t80) cc_final: 0.5559 (t80) REVERT: D 358 VAL cc_start: 0.6625 (t) cc_final: 0.6269 (p) REVERT: D 361 ILE cc_start: 0.5931 (OUTLIER) cc_final: 0.5577 (tt) REVERT: D 362 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5628 (mt) REVERT: D 370 ARG cc_start: 0.6197 (ttt180) cc_final: 0.5937 (mpt180) REVERT: D 373 LYS cc_start: 0.6893 (mtpp) cc_final: 0.6553 (tttp) REVERT: D 382 TYR cc_start: 0.4904 (m-80) cc_final: 0.3933 (m-80) REVERT: D 385 LYS cc_start: 0.6764 (ptmm) cc_final: 0.6191 (pttm) REVERT: D 423 ASP cc_start: 0.6766 (p0) cc_final: 0.6367 (p0) REVERT: E 236 MET cc_start: 0.3755 (mtp) cc_final: 0.3046 (tpp) REVERT: E 300 VAL cc_start: 0.6712 (p) cc_final: 0.6452 (t) REVERT: E 301 PHE cc_start: 0.6533 (t80) cc_final: 0.6257 (t80) REVERT: E 321 MET cc_start: 0.4633 (mmt) cc_final: 0.4204 (mmp) REVERT: F 68 MET cc_start: 0.1511 (ttm) cc_final: 0.0881 (mpt) REVERT: F 249 LYS cc_start: 0.5831 (mttp) cc_final: 0.5341 (mtmp) REVERT: F 328 VAL cc_start: 0.7561 (p) cc_final: 0.7115 (t) REVERT: G 236 MET cc_start: 0.3983 (mtp) cc_final: 0.3173 (tpp) REVERT: G 247 LEU cc_start: 0.6730 (tp) cc_final: 0.6274 (pp) REVERT: H 259 LEU cc_start: 0.5143 (tp) cc_final: 0.4843 (tm) REVERT: H 301 PHE cc_start: 0.6293 (t80) cc_final: 0.6019 (t80) outliers start: 126 outliers final: 57 residues processed: 529 average time/residue: 0.8134 time to fit residues: 515.7717 Evaluate side-chains 463 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 397 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 305 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 242 optimal weight: 0.9990 chunk 257 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 230 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 313 GLN B 213 HIS B 313 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 HIS C 313 GLN C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN E 91 ASN F 18 ASN F 91 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4924 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21078 Z= 0.194 Angle : 0.664 14.568 28651 Z= 0.331 Chirality : 0.043 0.271 3441 Planarity : 0.004 0.072 3553 Dihedral : 5.919 59.737 2830 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.14 % Allowed : 19.03 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 2623 helix: -0.14 (0.13), residues: 1371 sheet: 0.63 (0.43), residues: 156 loop : -1.83 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 331 HIS 0.003 0.001 HIS D 60 PHE 0.023 0.001 PHE C 334 TYR 0.030 0.001 TYR B 304 ARG 0.004 0.000 ARG D 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 427 time to evaluate : 2.294 Fit side-chains REVERT: A 21 MET cc_start: 0.6433 (mmt) cc_final: 0.5867 (mmm) REVERT: A 103 PHE cc_start: 0.6670 (t80) cc_final: 0.6421 (t80) REVERT: A 143 ILE cc_start: 0.7091 (pt) cc_final: 0.6566 (tp) REVERT: A 271 TRP cc_start: 0.7449 (t-100) cc_final: 0.6827 (t60) REVERT: A 280 ILE cc_start: 0.7529 (mm) cc_final: 0.7240 (mp) REVERT: A 343 SER cc_start: 0.7292 (p) cc_final: 0.6593 (m) REVERT: A 361 ILE cc_start: 0.6074 (mt) cc_final: 0.5567 (tt) REVERT: A 362 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.6084 (mp) REVERT: A 366 LEU cc_start: 0.6926 (mp) cc_final: 0.6286 (mt) REVERT: A 373 LYS cc_start: 0.6705 (tttt) cc_final: 0.6386 (ttpt) REVERT: A 382 TYR cc_start: 0.4674 (m-80) cc_final: 0.3917 (m-80) REVERT: A 423 ASP cc_start: 0.7176 (p0) cc_final: 0.6493 (p0) REVERT: A 447 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.5284 (mm) REVERT: A 454 ASP cc_start: 0.6740 (m-30) cc_final: 0.6277 (p0) REVERT: A 477 LEU cc_start: 0.7272 (mm) cc_final: 0.6701 (mt) REVERT: B 6 ILE cc_start: 0.6933 (OUTLIER) cc_final: 0.6628 (mt) REVERT: B 21 MET cc_start: 0.6642 (mmp) cc_final: 0.6174 (mmm) REVERT: B 54 TRP cc_start: 0.6868 (t-100) cc_final: 0.6648 (t-100) REVERT: B 103 PHE cc_start: 0.6878 (t80) cc_final: 0.6667 (t80) REVERT: B 188 ILE cc_start: 0.7209 (mm) cc_final: 0.6874 (pt) REVERT: B 190 LEU cc_start: 0.7006 (tm) cc_final: 0.6703 (tp) REVERT: B 201 TRP cc_start: 0.6738 (t60) cc_final: 0.6426 (t60) REVERT: B 236 TYR cc_start: 0.6968 (m-80) cc_final: 0.6624 (m-80) REVERT: B 277 ARG cc_start: 0.4900 (ptp90) cc_final: 0.3400 (ttt-90) REVERT: B 288 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6282 (tp) REVERT: B 294 LEU cc_start: 0.7753 (mt) cc_final: 0.7392 (mp) REVERT: B 373 LYS cc_start: 0.6737 (mtpp) cc_final: 0.6517 (ttpt) REVERT: B 382 TYR cc_start: 0.4949 (m-80) cc_final: 0.4176 (m-80) REVERT: B 391 LEU cc_start: 0.7315 (pp) cc_final: 0.6728 (tp) REVERT: B 453 ASN cc_start: 0.7191 (t0) cc_final: 0.6838 (t0) REVERT: B 466 PHE cc_start: 0.6476 (m-10) cc_final: 0.6274 (m-10) REVERT: B 477 LEU cc_start: 0.7049 (mm) cc_final: 0.6783 (tp) REVERT: C 8 ARG cc_start: 0.6432 (ttp-110) cc_final: 0.6156 (ttp-170) REVERT: C 12 LEU cc_start: 0.6732 (tm) cc_final: 0.6422 (pp) REVERT: C 103 PHE cc_start: 0.6851 (t80) cc_final: 0.6519 (t80) REVERT: C 120 LEU cc_start: 0.5501 (OUTLIER) cc_final: 0.5164 (tt) REVERT: C 190 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6584 (tp) REVERT: C 201 TRP cc_start: 0.6570 (t60) cc_final: 0.6274 (t60) REVERT: C 271 TRP cc_start: 0.7407 (t-100) cc_final: 0.6784 (t-100) REVERT: C 275 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6804 (tt0) REVERT: C 356 MET cc_start: 0.7987 (ptp) cc_final: 0.7500 (ptm) REVERT: C 363 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6691 (tt) REVERT: C 373 LYS cc_start: 0.6835 (mtpp) cc_final: 0.6251 (mtpp) REVERT: C 382 TYR cc_start: 0.4984 (m-80) cc_final: 0.2596 (m-80) REVERT: C 442 LEU cc_start: 0.4564 (OUTLIER) cc_final: 0.4196 (pt) REVERT: C 457 LYS cc_start: 0.7855 (mttt) cc_final: 0.7608 (mttt) REVERT: C 469 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6205 (pt) REVERT: D 8 ARG cc_start: 0.6346 (ttp80) cc_final: 0.6081 (ttp-110) REVERT: D 54 TRP cc_start: 0.7030 (t-100) cc_final: 0.6784 (t-100) REVERT: D 103 PHE cc_start: 0.6786 (t80) cc_final: 0.6533 (t80) REVERT: D 190 LEU cc_start: 0.6999 (tm) cc_final: 0.6606 (tp) REVERT: D 201 TRP cc_start: 0.6484 (t60) cc_final: 0.6202 (t60) REVERT: D 202 LEU cc_start: 0.6130 (OUTLIER) cc_final: 0.5635 (tp) REVERT: D 275 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6257 (tt0) REVERT: D 280 ILE cc_start: 0.7663 (mm) cc_final: 0.7418 (mp) REVERT: D 288 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6315 (tp) REVERT: D 312 PHE cc_start: 0.5909 (t80) cc_final: 0.5643 (t80) REVERT: D 358 VAL cc_start: 0.6760 (t) cc_final: 0.6369 (p) REVERT: D 361 ILE cc_start: 0.5882 (OUTLIER) cc_final: 0.5501 (tt) REVERT: D 362 LEU cc_start: 0.6246 (OUTLIER) cc_final: 0.5629 (mp) REVERT: D 370 ARG cc_start: 0.6381 (ttt180) cc_final: 0.6073 (ptm160) REVERT: D 382 TYR cc_start: 0.5145 (m-80) cc_final: 0.4404 (m-80) REVERT: D 385 LYS cc_start: 0.6811 (ptmm) cc_final: 0.6211 (pttm) REVERT: D 423 ASP cc_start: 0.7035 (p0) cc_final: 0.6686 (p0) REVERT: E 56 ASP cc_start: 0.0056 (OUTLIER) cc_final: -0.0391 (p0) REVERT: E 236 MET cc_start: 0.3892 (mtp) cc_final: 0.3062 (tpp) REVERT: E 270 LEU cc_start: 0.5536 (tt) cc_final: 0.5311 (tt) REVERT: E 288 GLU cc_start: 0.2886 (OUTLIER) cc_final: 0.1734 (pm20) REVERT: E 300 VAL cc_start: 0.6487 (p) cc_final: 0.6222 (t) REVERT: E 301 PHE cc_start: 0.6690 (t80) cc_final: 0.6372 (t80) REVERT: F 56 ASP cc_start: -0.0099 (OUTLIER) cc_final: -0.0522 (p0) REVERT: F 68 MET cc_start: 0.2028 (ttm) cc_final: 0.1469 (mpt) REVERT: F 236 MET cc_start: 0.3540 (OUTLIER) cc_final: 0.3168 (ppp) REVERT: F 301 PHE cc_start: 0.6315 (t80) cc_final: 0.5894 (t80) REVERT: F 302 ILE cc_start: 0.6821 (mt) cc_final: 0.6329 (mp) REVERT: F 358 LEU cc_start: 0.2963 (OUTLIER) cc_final: 0.2733 (tm) REVERT: G 56 ASP cc_start: 0.0401 (OUTLIER) cc_final: 0.0084 (p0) REVERT: G 236 MET cc_start: 0.3934 (OUTLIER) cc_final: 0.3723 (ppp) REVERT: G 247 LEU cc_start: 0.6967 (tp) cc_final: 0.6353 (pp) REVERT: G 327 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.5886 (tmt) REVERT: H 56 ASP cc_start: 0.0187 (OUTLIER) cc_final: -0.0265 (p0) REVERT: H 247 LEU cc_start: 0.6404 (tp) cc_final: 0.5949 (pp) REVERT: H 259 LEU cc_start: 0.5154 (tp) cc_final: 0.4871 (tm) REVERT: H 301 PHE cc_start: 0.6401 (t80) cc_final: 0.5901 (t80) REVERT: H 327 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.5679 (mpp) outliers start: 134 outliers final: 62 residues processed: 512 average time/residue: 0.8221 time to fit residues: 503.4884 Evaluate side-chains 484 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 397 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 236 MET Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 236 MET Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 327 MET Chi-restraints excluded: chain H residue 360 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 191 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 219 optimal weight: 0.0670 chunk 177 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 230 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 313 GLN A 437 ASN B 213 HIS B 313 GLN B 448 HIS C 213 HIS C 393 GLN C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN F 91 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4884 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21078 Z= 0.161 Angle : 0.623 12.760 28651 Z= 0.308 Chirality : 0.041 0.246 3441 Planarity : 0.004 0.072 3553 Dihedral : 5.572 57.363 2829 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 6.05 % Allowed : 20.08 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.98 (0.16), residues: 2623 helix: 0.05 (0.13), residues: 1377 sheet: 0.80 (0.42), residues: 156 loop : -1.77 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 331 HIS 0.002 0.001 HIS A 448 PHE 0.026 0.001 PHE C 334 TYR 0.035 0.001 TYR B 304 ARG 0.005 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 424 time to evaluate : 1.853 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.6499 (mmt) cc_final: 0.5912 (mmm) REVERT: A 47 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.6141 (mm) REVERT: A 103 PHE cc_start: 0.6633 (t80) cc_final: 0.6358 (t80) REVERT: A 143 ILE cc_start: 0.7034 (pt) cc_final: 0.6529 (tp) REVERT: A 271 TRP cc_start: 0.7467 (t-100) cc_final: 0.6811 (t60) REVERT: A 280 ILE cc_start: 0.7397 (mm) cc_final: 0.7106 (mp) REVERT: A 343 SER cc_start: 0.7187 (p) cc_final: 0.6980 (t) REVERT: A 361 ILE cc_start: 0.6172 (mt) cc_final: 0.5621 (tt) REVERT: A 376 VAL cc_start: 0.6923 (t) cc_final: 0.6719 (t) REVERT: A 382 TYR cc_start: 0.4580 (m-80) cc_final: 0.4127 (m-80) REVERT: A 391 LEU cc_start: 0.6824 (mp) cc_final: 0.6355 (mm) REVERT: A 423 ASP cc_start: 0.7194 (p0) cc_final: 0.6541 (p0) REVERT: A 447 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5539 (mp) REVERT: A 454 ASP cc_start: 0.6547 (m-30) cc_final: 0.6210 (p0) REVERT: A 477 LEU cc_start: 0.7341 (mm) cc_final: 0.6864 (mt) REVERT: B 21 MET cc_start: 0.6630 (mmp) cc_final: 0.6224 (mmm) REVERT: B 54 TRP cc_start: 0.6797 (t-100) cc_final: 0.6563 (t-100) REVERT: B 188 ILE cc_start: 0.7187 (mm) cc_final: 0.6835 (pt) REVERT: B 201 TRP cc_start: 0.6665 (t60) cc_final: 0.6313 (t60) REVERT: B 229 SER cc_start: 0.7749 (OUTLIER) cc_final: 0.7489 (p) REVERT: B 277 ARG cc_start: 0.4774 (ptp90) cc_final: 0.3684 (mtm-85) REVERT: B 288 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6268 (tp) REVERT: B 361 ILE cc_start: 0.6021 (tt) cc_final: 0.5796 (tt) REVERT: B 382 TYR cc_start: 0.4740 (m-80) cc_final: 0.3805 (m-80) REVERT: B 391 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6717 (tp) REVERT: B 453 ASN cc_start: 0.7081 (t0) cc_final: 0.6755 (t0) REVERT: B 466 PHE cc_start: 0.6334 (m-10) cc_final: 0.6116 (m-10) REVERT: B 477 LEU cc_start: 0.7063 (mm) cc_final: 0.6763 (tp) REVERT: C 8 ARG cc_start: 0.6425 (ttp-110) cc_final: 0.6178 (ttp-170) REVERT: C 103 PHE cc_start: 0.6832 (t80) cc_final: 0.6518 (t80) REVERT: C 120 LEU cc_start: 0.5629 (OUTLIER) cc_final: 0.5273 (tt) REVERT: C 190 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6481 (tp) REVERT: C 201 TRP cc_start: 0.6139 (t60) cc_final: 0.5879 (t60) REVERT: C 271 TRP cc_start: 0.7425 (t-100) cc_final: 0.6806 (t-100) REVERT: C 294 LEU cc_start: 0.7581 (mt) cc_final: 0.7196 (mp) REVERT: C 356 MET cc_start: 0.7971 (ptp) cc_final: 0.7493 (ptm) REVERT: C 363 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6529 (tt) REVERT: C 373 LYS cc_start: 0.6636 (mtpp) cc_final: 0.6118 (mtpp) REVERT: C 382 TYR cc_start: 0.4796 (m-80) cc_final: 0.2551 (m-80) REVERT: C 457 LYS cc_start: 0.7636 (mttt) cc_final: 0.7339 (mttt) REVERT: C 469 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6235 (pt) REVERT: D 21 MET cc_start: 0.6198 (mmt) cc_final: 0.5767 (mmm) REVERT: D 103 PHE cc_start: 0.6716 (t80) cc_final: 0.6423 (t80) REVERT: D 190 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6564 (tp) REVERT: D 201 TRP cc_start: 0.6407 (t60) cc_final: 0.6078 (t60) REVERT: D 202 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5517 (tp) REVERT: D 275 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6242 (tt0) REVERT: D 280 ILE cc_start: 0.7616 (mm) cc_final: 0.7358 (OUTLIER) REVERT: D 288 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6329 (tp) REVERT: D 312 PHE cc_start: 0.5818 (t80) cc_final: 0.5571 (t80) REVERT: D 358 VAL cc_start: 0.6637 (t) cc_final: 0.6323 (p) REVERT: D 361 ILE cc_start: 0.5909 (OUTLIER) cc_final: 0.5522 (tt) REVERT: D 362 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5505 (mp) REVERT: D 370 ARG cc_start: 0.6352 (ttt180) cc_final: 0.6002 (ptm160) REVERT: D 382 TYR cc_start: 0.4947 (m-80) cc_final: 0.4405 (m-80) REVERT: D 423 ASP cc_start: 0.7062 (p0) cc_final: 0.6704 (p0) REVERT: D 457 LYS cc_start: 0.7458 (mttt) cc_final: 0.7218 (mttt) REVERT: E 236 MET cc_start: 0.3560 (OUTLIER) cc_final: 0.2922 (tpp) REVERT: E 247 LEU cc_start: 0.6554 (tp) cc_final: 0.6109 (pp) REVERT: E 270 LEU cc_start: 0.5509 (tt) cc_final: 0.5288 (tt) REVERT: E 288 GLU cc_start: 0.2630 (OUTLIER) cc_final: 0.1591 (pm20) REVERT: E 300 VAL cc_start: 0.6424 (p) cc_final: 0.6141 (t) REVERT: E 301 PHE cc_start: 0.6598 (t80) cc_final: 0.6374 (t80) REVERT: E 321 MET cc_start: 0.5086 (mmp) cc_final: 0.4705 (mmp) REVERT: F 68 MET cc_start: 0.1837 (ttm) cc_final: 0.1172 (mpt) REVERT: F 301 PHE cc_start: 0.6104 (t80) cc_final: 0.5678 (t80) REVERT: F 302 ILE cc_start: 0.6710 (mt) cc_final: 0.6305 (mp) REVERT: F 349 SER cc_start: 0.6740 (t) cc_final: 0.6389 (p) REVERT: F 358 LEU cc_start: 0.3037 (OUTLIER) cc_final: 0.2153 (pp) REVERT: G 236 MET cc_start: 0.3978 (OUTLIER) cc_final: 0.3683 (ppp) REVERT: G 247 LEU cc_start: 0.6948 (tp) cc_final: 0.6339 (pp) REVERT: G 308 ASP cc_start: 0.3739 (OUTLIER) cc_final: 0.3078 (t0) REVERT: G 310 THR cc_start: 0.4057 (t) cc_final: 0.3770 (m) REVERT: G 327 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5584 (mpp) REVERT: H 247 LEU cc_start: 0.6438 (tp) cc_final: 0.5974 (pp) REVERT: H 259 LEU cc_start: 0.5155 (tp) cc_final: 0.4896 (tm) REVERT: H 301 PHE cc_start: 0.6116 (t80) cc_final: 0.5786 (t80) REVERT: H 302 ILE cc_start: 0.6786 (mt) cc_final: 0.6475 (mp) REVERT: H 327 MET cc_start: 0.6227 (OUTLIER) cc_final: 0.5660 (mpp) outliers start: 132 outliers final: 65 residues processed: 510 average time/residue: 0.8360 time to fit residues: 510.5383 Evaluate side-chains 477 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 391 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 189 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain G residue 236 MET Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 308 ASP Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 327 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 257 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 85 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 313 GLN B 213 HIS B 313 GLN B 448 HIS C 213 HIS C 393 GLN C 453 ASN D 213 HIS D 313 GLN E 91 ASN F 91 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4880 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21078 Z= 0.156 Angle : 0.628 12.333 28651 Z= 0.309 Chirality : 0.041 0.231 3441 Planarity : 0.004 0.069 3553 Dihedral : 5.318 54.340 2825 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.91 % Allowed : 21.14 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.91 (0.16), residues: 2623 helix: 0.11 (0.13), residues: 1388 sheet: 0.99 (0.43), residues: 156 loop : -1.78 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 331 HIS 0.003 0.001 HIS D 448 PHE 0.025 0.001 PHE B 291 TYR 0.033 0.001 TYR B 304 ARG 0.004 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 421 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6541 (mmt) cc_final: 0.6070 (mmm) REVERT: A 47 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.6109 (mm) REVERT: A 54 TRP cc_start: 0.7343 (t-100) cc_final: 0.7047 (t-100) REVERT: A 103 PHE cc_start: 0.6650 (t80) cc_final: 0.6404 (t80) REVERT: A 143 ILE cc_start: 0.7022 (pt) cc_final: 0.6496 (tp) REVERT: A 201 TRP cc_start: 0.6181 (t60) cc_final: 0.5757 (t60) REVERT: A 271 TRP cc_start: 0.7522 (t-100) cc_final: 0.6908 (t60) REVERT: A 280 ILE cc_start: 0.7417 (mm) cc_final: 0.7135 (mp) REVERT: A 361 ILE cc_start: 0.6078 (mt) cc_final: 0.5547 (tt) REVERT: A 391 LEU cc_start: 0.6765 (mp) cc_final: 0.6334 (mm) REVERT: A 395 VAL cc_start: 0.7586 (OUTLIER) cc_final: 0.7221 (p) REVERT: A 423 ASP cc_start: 0.7202 (p0) cc_final: 0.6540 (p0) REVERT: A 477 LEU cc_start: 0.7378 (mm) cc_final: 0.6828 (mt) REVERT: B 21 MET cc_start: 0.6530 (mmp) cc_final: 0.6061 (mmm) REVERT: B 54 TRP cc_start: 0.6777 (t-100) cc_final: 0.6535 (t-100) REVERT: B 188 ILE cc_start: 0.7190 (mm) cc_final: 0.6816 (pt) REVERT: B 201 TRP cc_start: 0.6657 (t60) cc_final: 0.6306 (t60) REVERT: B 236 TYR cc_start: 0.6832 (m-80) cc_final: 0.6527 (m-80) REVERT: B 277 ARG cc_start: 0.4662 (ptp90) cc_final: 0.3528 (mtm-85) REVERT: B 288 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6254 (tp) REVERT: B 294 LEU cc_start: 0.7740 (mt) cc_final: 0.7368 (mp) REVERT: B 361 ILE cc_start: 0.5912 (tt) cc_final: 0.5667 (tt) REVERT: B 373 LYS cc_start: 0.5856 (tttm) cc_final: 0.5606 (tttm) REVERT: B 382 TYR cc_start: 0.4557 (m-80) cc_final: 0.2942 (m-80) REVERT: B 391 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6739 (tp) REVERT: B 453 ASN cc_start: 0.7089 (t0) cc_final: 0.6725 (t0) REVERT: B 477 LEU cc_start: 0.7088 (mm) cc_final: 0.6821 (tp) REVERT: C 8 ARG cc_start: 0.6307 (ttp-110) cc_final: 0.6086 (ttp-170) REVERT: C 12 LEU cc_start: 0.6586 (tm) cc_final: 0.6151 (pp) REVERT: C 103 PHE cc_start: 0.6859 (t80) cc_final: 0.6546 (t80) REVERT: C 120 LEU cc_start: 0.5511 (OUTLIER) cc_final: 0.5177 (tt) REVERT: C 190 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6377 (tp) REVERT: C 201 TRP cc_start: 0.6105 (t60) cc_final: 0.5856 (t60) REVERT: C 271 TRP cc_start: 0.7379 (t-100) cc_final: 0.6817 (t-100) REVERT: C 356 MET cc_start: 0.7972 (ptp) cc_final: 0.7495 (ptm) REVERT: C 363 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6475 (tt) REVERT: C 373 LYS cc_start: 0.6644 (mtpp) cc_final: 0.6118 (mtpp) REVERT: C 382 TYR cc_start: 0.4766 (m-80) cc_final: 0.2634 (m-80) REVERT: C 423 ASP cc_start: 0.6718 (p0) cc_final: 0.6364 (p0) REVERT: C 457 LYS cc_start: 0.7725 (mttt) cc_final: 0.7435 (mttt) REVERT: C 469 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6185 (pt) REVERT: D 8 ARG cc_start: 0.6216 (ttp-110) cc_final: 0.5960 (ttp-170) REVERT: D 21 MET cc_start: 0.6365 (mmt) cc_final: 0.6060 (mmm) REVERT: D 103 PHE cc_start: 0.6658 (t80) cc_final: 0.6389 (t80) REVERT: D 190 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6440 (tp) REVERT: D 201 TRP cc_start: 0.6265 (t60) cc_final: 0.5948 (t60) REVERT: D 202 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5531 (tp) REVERT: D 275 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.6195 (tt0) REVERT: D 280 ILE cc_start: 0.7620 (mm) cc_final: 0.7365 (OUTLIER) REVERT: D 288 LEU cc_start: 0.6644 (OUTLIER) cc_final: 0.6294 (tp) REVERT: D 294 LEU cc_start: 0.7595 (mt) cc_final: 0.7222 (mp) REVERT: D 312 PHE cc_start: 0.5764 (t80) cc_final: 0.5525 (t80) REVERT: D 358 VAL cc_start: 0.6623 (t) cc_final: 0.6350 (p) REVERT: D 361 ILE cc_start: 0.5926 (OUTLIER) cc_final: 0.5495 (tt) REVERT: D 362 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5441 (mp) REVERT: D 370 ARG cc_start: 0.6361 (ttt180) cc_final: 0.6026 (ptm160) REVERT: D 382 TYR cc_start: 0.4885 (m-80) cc_final: 0.4386 (m-80) REVERT: D 423 ASP cc_start: 0.7170 (p0) cc_final: 0.6923 (p0) REVERT: D 447 LEU cc_start: 0.5705 (OUTLIER) cc_final: 0.5446 (mt) REVERT: E 56 ASP cc_start: 0.0437 (OUTLIER) cc_final: 0.0109 (p0) REVERT: E 247 LEU cc_start: 0.6547 (tp) cc_final: 0.6057 (pp) REVERT: E 260 ILE cc_start: 0.5842 (mt) cc_final: 0.5377 (mm) REVERT: E 288 GLU cc_start: 0.3231 (OUTLIER) cc_final: 0.2066 (pm20) REVERT: E 300 VAL cc_start: 0.6355 (p) cc_final: 0.6050 (t) REVERT: F 56 ASP cc_start: 0.0179 (OUTLIER) cc_final: -0.0203 (p0) REVERT: F 68 MET cc_start: 0.1394 (ttm) cc_final: 0.1045 (mmm) REVERT: F 247 LEU cc_start: 0.6712 (tp) cc_final: 0.6117 (pp) REVERT: F 249 LYS cc_start: 0.5427 (mttp) cc_final: 0.5099 (pttt) REVERT: F 302 ILE cc_start: 0.6855 (mt) cc_final: 0.6460 (mm) REVERT: F 349 SER cc_start: 0.6748 (t) cc_final: 0.6425 (p) REVERT: G 56 ASP cc_start: 0.0482 (OUTLIER) cc_final: 0.0255 (p0) REVERT: G 236 MET cc_start: 0.4150 (OUTLIER) cc_final: 0.3828 (ppp) REVERT: G 247 LEU cc_start: 0.6962 (tp) cc_final: 0.6344 (pp) REVERT: G 308 ASP cc_start: 0.3795 (OUTLIER) cc_final: 0.3082 (t0) REVERT: G 310 THR cc_start: 0.4235 (t) cc_final: 0.3956 (m) REVERT: G 327 MET cc_start: 0.6339 (OUTLIER) cc_final: 0.5737 (mpp) REVERT: H 56 ASP cc_start: 0.0498 (OUTLIER) cc_final: 0.0196 (p0) REVERT: H 247 LEU cc_start: 0.6484 (tp) cc_final: 0.6036 (pp) REVERT: H 249 LYS cc_start: 0.5024 (mttp) cc_final: 0.4697 (pttt) REVERT: H 259 LEU cc_start: 0.5200 (tp) cc_final: 0.4910 (tm) REVERT: H 275 GLU cc_start: 0.3710 (tp30) cc_final: 0.3485 (mm-30) REVERT: H 327 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.5664 (mpp) outliers start: 129 outliers final: 66 residues processed: 505 average time/residue: 0.8362 time to fit residues: 506.2930 Evaluate side-chains 480 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 391 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 236 MET Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 308 ASP Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 327 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 187 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 216 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 256 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 313 GLN B 213 HIS ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 HIS C 213 HIS C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN G 253 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4981 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21078 Z= 0.222 Angle : 0.711 14.729 28651 Z= 0.355 Chirality : 0.044 0.234 3441 Planarity : 0.005 0.068 3553 Dihedral : 5.708 52.511 2822 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 6.10 % Allowed : 22.33 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.15), residues: 2623 helix: -0.31 (0.13), residues: 1379 sheet: 0.55 (0.40), residues: 176 loop : -1.99 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 331 HIS 0.005 0.001 HIS D 448 PHE 0.026 0.002 PHE C 334 TYR 0.037 0.002 TYR B 304 ARG 0.005 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 422 time to evaluate : 2.298 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.6468 (mmt) cc_final: 0.6044 (mmm) REVERT: A 47 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5984 (mm) REVERT: A 54 TRP cc_start: 0.7354 (t-100) cc_final: 0.7057 (t-100) REVERT: A 103 PHE cc_start: 0.6698 (t80) cc_final: 0.6441 (t80) REVERT: A 143 ILE cc_start: 0.7045 (pt) cc_final: 0.6499 (tp) REVERT: A 201 TRP cc_start: 0.6259 (t60) cc_final: 0.5939 (t60) REVERT: A 271 TRP cc_start: 0.7552 (t-100) cc_final: 0.7007 (t60) REVERT: A 280 ILE cc_start: 0.7543 (mm) cc_final: 0.7264 (mp) REVERT: A 361 ILE cc_start: 0.6159 (mt) cc_final: 0.5700 (tt) REVERT: A 373 LYS cc_start: 0.6778 (tttt) cc_final: 0.6330 (ttpp) REVERT: A 382 TYR cc_start: 0.5181 (m-80) cc_final: 0.4217 (m-80) REVERT: A 391 LEU cc_start: 0.6985 (mp) cc_final: 0.6475 (mm) REVERT: A 395 VAL cc_start: 0.7382 (OUTLIER) cc_final: 0.6970 (p) REVERT: A 423 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6376 (p0) REVERT: A 477 LEU cc_start: 0.7244 (mm) cc_final: 0.6706 (mt) REVERT: B 8 ARG cc_start: 0.6329 (ttp-110) cc_final: 0.5867 (ttp80) REVERT: B 21 MET cc_start: 0.6576 (mmp) cc_final: 0.6138 (mmm) REVERT: B 188 ILE cc_start: 0.7144 (mm) cc_final: 0.6774 (pt) REVERT: B 201 TRP cc_start: 0.6809 (t60) cc_final: 0.6504 (t60) REVERT: B 277 ARG cc_start: 0.4880 (ptp90) cc_final: 0.3399 (mtm-85) REVERT: B 288 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6248 (tp) REVERT: B 293 LEU cc_start: 0.7353 (mm) cc_final: 0.6657 (pp) REVERT: B 334 PHE cc_start: 0.6177 (t80) cc_final: 0.5806 (t80) REVERT: B 373 LYS cc_start: 0.6147 (tttm) cc_final: 0.5841 (tttm) REVERT: B 382 TYR cc_start: 0.5515 (m-80) cc_final: 0.4093 (m-80) REVERT: B 391 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6895 (tp) REVERT: B 453 ASN cc_start: 0.7324 (t0) cc_final: 0.6889 (t0) REVERT: C 8 ARG cc_start: 0.6415 (ttp-110) cc_final: 0.6064 (ttp80) REVERT: C 103 PHE cc_start: 0.6906 (t80) cc_final: 0.6598 (t80) REVERT: C 120 LEU cc_start: 0.5405 (OUTLIER) cc_final: 0.5151 (tt) REVERT: C 189 TYR cc_start: 0.5976 (OUTLIER) cc_final: 0.5449 (t80) REVERT: C 190 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6494 (tp) REVERT: C 201 TRP cc_start: 0.6190 (t60) cc_final: 0.5926 (t60) REVERT: C 271 TRP cc_start: 0.7373 (t-100) cc_final: 0.6755 (t-100) REVERT: C 294 LEU cc_start: 0.7679 (mt) cc_final: 0.7276 (mp) REVERT: C 356 MET cc_start: 0.8070 (ptp) cc_final: 0.7692 (ptm) REVERT: C 363 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6669 (tt) REVERT: C 373 LYS cc_start: 0.6830 (mtpp) cc_final: 0.6141 (mtpp) REVERT: C 382 TYR cc_start: 0.5315 (m-80) cc_final: 0.4645 (m-80) REVERT: C 457 LYS cc_start: 0.7844 (mttt) cc_final: 0.7640 (mttt) REVERT: C 469 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6275 (pt) REVERT: C 478 LEU cc_start: 0.7123 (pp) cc_final: 0.6800 (pt) REVERT: D 8 ARG cc_start: 0.6226 (ttp-110) cc_final: 0.5989 (ttp80) REVERT: D 21 MET cc_start: 0.6421 (mmt) cc_final: 0.6176 (mmm) REVERT: D 103 PHE cc_start: 0.6746 (t80) cc_final: 0.6474 (t80) REVERT: D 280 ILE cc_start: 0.7655 (mm) cc_final: 0.7424 (mp) REVERT: D 288 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6212 (tp) REVERT: D 312 PHE cc_start: 0.6146 (t80) cc_final: 0.5847 (t80) REVERT: D 358 VAL cc_start: 0.6892 (t) cc_final: 0.6556 (p) REVERT: D 361 ILE cc_start: 0.5935 (OUTLIER) cc_final: 0.5541 (tt) REVERT: D 362 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.5668 (mp) REVERT: D 370 ARG cc_start: 0.6486 (ttt180) cc_final: 0.6087 (ptm160) REVERT: D 382 TYR cc_start: 0.5360 (m-80) cc_final: 0.4415 (m-80) REVERT: D 447 LEU cc_start: 0.5914 (OUTLIER) cc_final: 0.5648 (mp) REVERT: E 56 ASP cc_start: 0.0384 (OUTLIER) cc_final: -0.0051 (p0) REVERT: E 247 LEU cc_start: 0.6703 (tp) cc_final: 0.6134 (pp) REVERT: E 249 LYS cc_start: 0.5585 (mttm) cc_final: 0.5143 (pttt) REVERT: E 300 VAL cc_start: 0.6481 (p) cc_final: 0.6090 (t) REVERT: E 301 PHE cc_start: 0.6506 (t80) cc_final: 0.6003 (t80) REVERT: F 56 ASP cc_start: 0.0042 (OUTLIER) cc_final: -0.0406 (p0) REVERT: F 247 LEU cc_start: 0.6734 (tp) cc_final: 0.6168 (pp) REVERT: F 293 GLU cc_start: 0.4527 (mm-30) cc_final: 0.4289 (mp0) REVERT: F 302 ILE cc_start: 0.6651 (mt) cc_final: 0.6381 (mp) REVERT: G 56 ASP cc_start: 0.0279 (OUTLIER) cc_final: -0.0190 (p0) REVERT: G 247 LEU cc_start: 0.7059 (tp) cc_final: 0.6339 (pp) REVERT: G 308 ASP cc_start: 0.3761 (OUTLIER) cc_final: 0.3194 (t0) REVERT: G 327 MET cc_start: 0.6380 (OUTLIER) cc_final: 0.5804 (tmt) REVERT: H 56 ASP cc_start: 0.0528 (OUTLIER) cc_final: -0.0048 (p0) REVERT: H 243 ILE cc_start: 0.7626 (mt) cc_final: 0.7171 (tt) REVERT: H 247 LEU cc_start: 0.6390 (tp) cc_final: 0.5932 (pp) REVERT: H 259 LEU cc_start: 0.5228 (tp) cc_final: 0.4845 (tm) REVERT: H 292 GLU cc_start: 0.4895 (tt0) cc_final: 0.4497 (pt0) REVERT: H 327 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.5671 (tmt) outliers start: 133 outliers final: 71 residues processed: 513 average time/residue: 0.8269 time to fit residues: 507.8768 Evaluate side-chains 488 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 396 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 189 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 308 ASP Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 327 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 chunk 126 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 201 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 313 GLN B 213 HIS B 313 GLN B 448 HIS C 213 HIS C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN F 84 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4906 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21078 Z= 0.165 Angle : 0.681 12.572 28651 Z= 0.326 Chirality : 0.042 0.228 3441 Planarity : 0.004 0.071 3553 Dihedral : 5.408 54.976 2822 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.23 % Allowed : 23.20 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 2623 helix: -0.06 (0.13), residues: 1390 sheet: 1.12 (0.43), residues: 156 loop : -1.89 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 331 HIS 0.003 0.001 HIS D 448 PHE 0.026 0.001 PHE B 291 TYR 0.038 0.001 TYR B 304 ARG 0.004 0.000 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 414 time to evaluate : 2.317 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.6497 (mmt) cc_final: 0.6019 (mmm) REVERT: A 47 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6164 (mm) REVERT: A 54 TRP cc_start: 0.7323 (t-100) cc_final: 0.7022 (t-100) REVERT: A 103 PHE cc_start: 0.6669 (t80) cc_final: 0.6423 (t80) REVERT: A 143 ILE cc_start: 0.6802 (pt) cc_final: 0.6274 (tp) REVERT: A 201 TRP cc_start: 0.6160 (t60) cc_final: 0.5853 (t60) REVERT: A 271 TRP cc_start: 0.7509 (t-100) cc_final: 0.6988 (t60) REVERT: A 280 ILE cc_start: 0.7456 (mm) cc_final: 0.7165 (mp) REVERT: A 294 LEU cc_start: 0.7730 (mt) cc_final: 0.7308 (mp) REVERT: A 361 ILE cc_start: 0.6092 (mt) cc_final: 0.5462 (tt) REVERT: A 373 LYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6185 (ttpp) REVERT: A 382 TYR cc_start: 0.4615 (m-80) cc_final: 0.3888 (m-80) REVERT: A 391 LEU cc_start: 0.6794 (mp) cc_final: 0.6365 (mm) REVERT: A 395 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7322 (p) REVERT: A 423 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6499 (p0) REVERT: A 435 LEU cc_start: 0.6009 (mt) cc_final: 0.5128 (pt) REVERT: A 469 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6002 (mm) REVERT: A 477 LEU cc_start: 0.7272 (mm) cc_final: 0.6743 (mt) REVERT: B 8 ARG cc_start: 0.6426 (ttp-110) cc_final: 0.6029 (ttp80) REVERT: B 21 MET cc_start: 0.6507 (mmp) cc_final: 0.6029 (mmm) REVERT: B 188 ILE cc_start: 0.7090 (mm) cc_final: 0.6720 (pt) REVERT: B 201 TRP cc_start: 0.6792 (t60) cc_final: 0.6469 (t60) REVERT: B 277 ARG cc_start: 0.4689 (OUTLIER) cc_final: 0.3508 (mtm-85) REVERT: B 288 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6250 (tp) REVERT: B 294 LEU cc_start: 0.7757 (mt) cc_final: 0.7385 (mp) REVERT: B 373 LYS cc_start: 0.5817 (tttm) cc_final: 0.5589 (tttm) REVERT: B 379 ARG cc_start: 0.6917 (ttm170) cc_final: 0.6644 (ttm170) REVERT: B 382 TYR cc_start: 0.4803 (m-80) cc_final: 0.3435 (m-80) REVERT: B 391 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6890 (tp) REVERT: B 423 ASP cc_start: 0.7222 (OUTLIER) cc_final: 0.6997 (p0) REVERT: B 453 ASN cc_start: 0.7072 (t0) cc_final: 0.6737 (t0) REVERT: C 103 PHE cc_start: 0.6821 (t80) cc_final: 0.6506 (t80) REVERT: C 120 LEU cc_start: 0.5395 (OUTLIER) cc_final: 0.5191 (tt) REVERT: C 201 TRP cc_start: 0.6125 (t60) cc_final: 0.5881 (t60) REVERT: C 205 MET cc_start: 0.3793 (pmm) cc_final: 0.3447 (ptp) REVERT: C 271 TRP cc_start: 0.7306 (t-100) cc_final: 0.6692 (t-100) REVERT: C 294 LEU cc_start: 0.7617 (mt) cc_final: 0.7330 (mp) REVERT: C 356 MET cc_start: 0.7972 (ptp) cc_final: 0.7504 (ptm) REVERT: C 373 LYS cc_start: 0.6623 (mtpp) cc_final: 0.6236 (tttm) REVERT: C 382 TYR cc_start: 0.4903 (m-80) cc_final: 0.2706 (m-80) REVERT: C 457 LYS cc_start: 0.7814 (mttt) cc_final: 0.7452 (mttt) REVERT: C 469 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6200 (pt) REVERT: C 478 LEU cc_start: 0.7156 (pp) cc_final: 0.6833 (pt) REVERT: D 8 ARG cc_start: 0.6174 (ttp-110) cc_final: 0.5949 (ttp80) REVERT: D 103 PHE cc_start: 0.6689 (t80) cc_final: 0.6399 (t80) REVERT: D 238 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6630 (tt) REVERT: D 280 ILE cc_start: 0.7665 (mm) cc_final: 0.7407 (mp) REVERT: D 288 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6304 (tp) REVERT: D 294 LEU cc_start: 0.7638 (mt) cc_final: 0.7248 (mp) REVERT: D 358 VAL cc_start: 0.6716 (t) cc_final: 0.6364 (p) REVERT: D 361 ILE cc_start: 0.6005 (OUTLIER) cc_final: 0.5572 (tt) REVERT: D 362 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5523 (mp) REVERT: D 370 ARG cc_start: 0.6362 (ttt180) cc_final: 0.5989 (mpt180) REVERT: D 382 TYR cc_start: 0.5105 (m-80) cc_final: 0.2937 (t80) REVERT: D 447 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5532 (mt) REVERT: D 471 ILE cc_start: 0.7060 (pt) cc_final: 0.6828 (mp) REVERT: E 242 ASN cc_start: 0.7063 (OUTLIER) cc_final: 0.6586 (m-40) REVERT: E 247 LEU cc_start: 0.6635 (tp) cc_final: 0.6087 (pp) REVERT: E 249 LYS cc_start: 0.5304 (mttm) cc_final: 0.4822 (pttt) REVERT: E 288 GLU cc_start: 0.3049 (OUTLIER) cc_final: 0.1989 (pm20) REVERT: E 300 VAL cc_start: 0.6315 (p) cc_final: 0.5932 (t) REVERT: E 301 PHE cc_start: 0.6287 (t80) cc_final: 0.6072 (t80) REVERT: F 242 ASN cc_start: 0.7281 (m-40) cc_final: 0.6741 (m-40) REVERT: F 247 LEU cc_start: 0.6689 (tp) cc_final: 0.6100 (pp) REVERT: F 249 LYS cc_start: 0.5428 (mttm) cc_final: 0.4942 (pttt) REVERT: F 302 ILE cc_start: 0.6541 (mt) cc_final: 0.6257 (mm) REVERT: G 247 LEU cc_start: 0.6985 (tp) cc_final: 0.6340 (pp) REVERT: G 292 GLU cc_start: 0.4997 (tt0) cc_final: 0.4502 (tp30) REVERT: G 308 ASP cc_start: 0.3580 (OUTLIER) cc_final: 0.2962 (t0) REVERT: G 327 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.5670 (tmt) REVERT: H 243 ILE cc_start: 0.7548 (mt) cc_final: 0.7085 (tt) REVERT: H 247 LEU cc_start: 0.6335 (tp) cc_final: 0.5930 (pp) REVERT: H 249 LYS cc_start: 0.5033 (mttp) cc_final: 0.4735 (pttt) REVERT: H 259 LEU cc_start: 0.5156 (tp) cc_final: 0.4825 (tm) REVERT: H 275 GLU cc_start: 0.4976 (mt-10) cc_final: 0.4414 (mt-10) REVERT: H 292 GLU cc_start: 0.4756 (tt0) cc_final: 0.4412 (pt0) REVERT: H 327 MET cc_start: 0.6171 (OUTLIER) cc_final: 0.5530 (tmt) outliers start: 114 outliers final: 62 residues processed: 486 average time/residue: 0.8414 time to fit residues: 487.4476 Evaluate side-chains 469 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 386 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 189 TYR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain E residue 242 ASN Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 308 ASP Chi-restraints excluded: chain G residue 327 MET Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 327 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 0.0070 chunk 245 optimal weight: 0.6980 chunk 224 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 215 optimal weight: 0.0970 chunk 225 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 313 GLN B 213 HIS B 313 GLN B 448 HIS C 213 HIS C 453 ASN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4942 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21078 Z= 0.188 Angle : 0.703 13.182 28651 Z= 0.342 Chirality : 0.043 0.220 3441 Planarity : 0.004 0.070 3553 Dihedral : 5.490 56.277 2822 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.09 % Allowed : 24.25 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 2623 helix: -0.16 (0.13), residues: 1391 sheet: 0.76 (0.39), residues: 180 loop : -1.99 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 331 HIS 0.004 0.001 HIS D 448 PHE 0.029 0.002 PHE B 334 TYR 0.035 0.001 TYR B 304 ARG 0.004 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 405 time to evaluate : 1.987 Fit side-chains revert: symmetry clash REVERT: A 47 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6198 (mm) REVERT: A 54 TRP cc_start: 0.7214 (t-100) cc_final: 0.6902 (t-100) REVERT: A 103 PHE cc_start: 0.6660 (t80) cc_final: 0.6400 (t80) REVERT: A 143 ILE cc_start: 0.6726 (pt) cc_final: 0.6238 (tp) REVERT: A 201 TRP cc_start: 0.6213 (t60) cc_final: 0.5900 (t60) REVERT: A 271 TRP cc_start: 0.7559 (t-100) cc_final: 0.7093 (t60) REVERT: A 280 ILE cc_start: 0.7485 (mm) cc_final: 0.7187 (mp) REVERT: A 361 ILE cc_start: 0.6183 (mt) cc_final: 0.5534 (tt) REVERT: A 373 LYS cc_start: 0.6764 (tttt) cc_final: 0.6319 (ttpp) REVERT: A 382 TYR cc_start: 0.4935 (m-80) cc_final: 0.4007 (m-80) REVERT: A 391 LEU cc_start: 0.6923 (mp) cc_final: 0.6431 (mm) REVERT: A 395 VAL cc_start: 0.7646 (OUTLIER) cc_final: 0.7337 (p) REVERT: A 423 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6448 (p0) REVERT: A 435 LEU cc_start: 0.6080 (mt) cc_final: 0.5153 (pt) REVERT: A 477 LEU cc_start: 0.7268 (mm) cc_final: 0.6728 (mt) REVERT: B 8 ARG cc_start: 0.6399 (ttp-110) cc_final: 0.6001 (ttp80) REVERT: B 21 MET cc_start: 0.6503 (mmp) cc_final: 0.6039 (mmm) REVERT: B 102 PHE cc_start: 0.6499 (m-80) cc_final: 0.6188 (m-80) REVERT: B 188 ILE cc_start: 0.7115 (mm) cc_final: 0.6737 (pt) REVERT: B 201 TRP cc_start: 0.6493 (t60) cc_final: 0.6215 (t60) REVERT: B 277 ARG cc_start: 0.4757 (OUTLIER) cc_final: 0.3241 (mtm-85) REVERT: B 288 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6229 (tp) REVERT: B 294 LEU cc_start: 0.7772 (mt) cc_final: 0.7399 (mp) REVERT: B 361 ILE cc_start: 0.5829 (mt) cc_final: 0.5424 (tt) REVERT: B 373 LYS cc_start: 0.5946 (tttm) cc_final: 0.5693 (tttm) REVERT: B 382 TYR cc_start: 0.4925 (m-80) cc_final: 0.3714 (m-80) REVERT: B 391 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6918 (tp) REVERT: B 423 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6622 (p0) REVERT: B 453 ASN cc_start: 0.7225 (t0) cc_final: 0.6652 (t0) REVERT: C 8 ARG cc_start: 0.6163 (ttp-110) cc_final: 0.5911 (ttp80) REVERT: C 103 PHE cc_start: 0.6862 (t80) cc_final: 0.6547 (t80) REVERT: C 201 TRP cc_start: 0.6180 (t60) cc_final: 0.5936 (t60) REVERT: C 205 MET cc_start: 0.4008 (pmm) cc_final: 0.3540 (ptp) REVERT: C 271 TRP cc_start: 0.7355 (t-100) cc_final: 0.6768 (t-100) REVERT: C 294 LEU cc_start: 0.7643 (mt) cc_final: 0.7350 (mp) REVERT: C 356 MET cc_start: 0.8024 (ptp) cc_final: 0.7607 (ptm) REVERT: C 363 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6586 (tt) REVERT: C 373 LYS cc_start: 0.6739 (mtpp) cc_final: 0.6338 (tttt) REVERT: C 382 TYR cc_start: 0.4979 (m-80) cc_final: 0.2703 (m-80) REVERT: C 457 LYS cc_start: 0.7731 (mttt) cc_final: 0.7419 (mttt) REVERT: C 469 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6155 (pt) REVERT: C 478 LEU cc_start: 0.7162 (pp) cc_final: 0.6844 (pt) REVERT: D 6 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6952 (pt) REVERT: D 8 ARG cc_start: 0.6213 (ttp-110) cc_final: 0.5978 (ttp80) REVERT: D 21 MET cc_start: 0.6486 (mmp) cc_final: 0.6113 (mmm) REVERT: D 103 PHE cc_start: 0.6708 (t80) cc_final: 0.6413 (t80) REVERT: D 205 MET cc_start: 0.4409 (pmm) cc_final: 0.3961 (ptp) REVERT: D 280 ILE cc_start: 0.7712 (mm) cc_final: 0.7475 (mp) REVERT: D 288 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6318 (tp) REVERT: D 294 LEU cc_start: 0.7631 (mt) cc_final: 0.7243 (mp) REVERT: D 358 VAL cc_start: 0.6793 (t) cc_final: 0.6428 (p) REVERT: D 361 ILE cc_start: 0.5966 (OUTLIER) cc_final: 0.5524 (tt) REVERT: D 362 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5553 (mp) REVERT: D 370 ARG cc_start: 0.6473 (ttt180) cc_final: 0.6091 (ptm160) REVERT: D 382 TYR cc_start: 0.5124 (m-80) cc_final: 0.4395 (m-80) REVERT: D 447 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5694 (mt) REVERT: D 471 ILE cc_start: 0.7068 (pt) cc_final: 0.6842 (mp) REVERT: D 477 LEU cc_start: 0.7207 (mm) cc_final: 0.6928 (mt) REVERT: E 242 ASN cc_start: 0.6925 (OUTLIER) cc_final: 0.6501 (m-40) REVERT: E 247 LEU cc_start: 0.6660 (tp) cc_final: 0.6100 (pp) REVERT: E 249 LYS cc_start: 0.5343 (mttm) cc_final: 0.4891 (pttt) REVERT: E 288 GLU cc_start: 0.3191 (OUTLIER) cc_final: 0.1996 (pm20) REVERT: E 300 VAL cc_start: 0.6249 (p) cc_final: 0.5909 (t) REVERT: F 56 ASP cc_start: 0.0178 (OUTLIER) cc_final: -0.0206 (p0) REVERT: F 247 LEU cc_start: 0.6600 (tp) cc_final: 0.6074 (pp) REVERT: F 249 LYS cc_start: 0.5396 (mttm) cc_final: 0.4961 (pttt) REVERT: F 302 ILE cc_start: 0.6496 (mt) cc_final: 0.6232 (mm) REVERT: G 56 ASP cc_start: 0.0061 (OUTLIER) cc_final: -0.0175 (p0) REVERT: G 247 LEU cc_start: 0.7049 (tp) cc_final: 0.6343 (pp) REVERT: G 292 GLU cc_start: 0.5004 (tt0) cc_final: 0.4505 (tp30) REVERT: G 308 ASP cc_start: 0.3677 (OUTLIER) cc_final: 0.3050 (t0) REVERT: H 56 ASP cc_start: 0.0205 (OUTLIER) cc_final: -0.0085 (p0) REVERT: H 243 ILE cc_start: 0.7602 (mt) cc_final: 0.7133 (tt) REVERT: H 247 LEU cc_start: 0.6367 (tp) cc_final: 0.5927 (pp) REVERT: H 249 LYS cc_start: 0.5036 (mttp) cc_final: 0.4636 (pttt) REVERT: H 259 LEU cc_start: 0.5244 (tp) cc_final: 0.4864 (tm) REVERT: H 275 GLU cc_start: 0.5050 (mt-10) cc_final: 0.4314 (mm-30) REVERT: H 292 GLU cc_start: 0.4853 (tt0) cc_final: 0.4503 (pt0) REVERT: H 327 MET cc_start: 0.6213 (OUTLIER) cc_final: 0.5613 (tmt) outliers start: 111 outliers final: 64 residues processed: 471 average time/residue: 0.8643 time to fit residues: 483.2093 Evaluate side-chains 476 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 391 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 189 TYR Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain E residue 242 ASN Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 308 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 327 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 243 optimal weight: 20.0000 chunk 211 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 313 GLN B 213 HIS ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 HIS C 213 HIS C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4988 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21078 Z= 0.231 Angle : 0.745 14.329 28651 Z= 0.367 Chirality : 0.045 0.227 3441 Planarity : 0.005 0.068 3553 Dihedral : 5.739 56.861 2822 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.36 % Allowed : 24.81 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 2623 helix: -0.38 (0.13), residues: 1386 sheet: 0.49 (0.39), residues: 180 loop : -2.09 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 331 HIS 0.005 0.001 HIS D 448 PHE 0.025 0.002 PHE C 312 TYR 0.034 0.002 TYR B 304 ARG 0.004 0.001 ARG A 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 397 time to evaluate : 2.001 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.6672 (mmp) cc_final: 0.6219 (mmm) REVERT: A 47 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6242 (mm) REVERT: A 54 TRP cc_start: 0.7216 (t-100) cc_final: 0.6913 (t-100) REVERT: A 103 PHE cc_start: 0.6709 (t80) cc_final: 0.6436 (t80) REVERT: A 143 ILE cc_start: 0.6992 (pt) cc_final: 0.6513 (tp) REVERT: A 201 TRP cc_start: 0.6314 (t60) cc_final: 0.5994 (t60) REVERT: A 271 TRP cc_start: 0.7581 (t-100) cc_final: 0.7151 (t60) REVERT: A 280 ILE cc_start: 0.7540 (mm) cc_final: 0.7247 (mp) REVERT: A 361 ILE cc_start: 0.6116 (mt) cc_final: 0.5508 (tt) REVERT: A 373 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6438 (ttpp) REVERT: A 382 TYR cc_start: 0.5078 (m-80) cc_final: 0.4012 (m-80) REVERT: A 391 LEU cc_start: 0.7131 (mp) cc_final: 0.6592 (mm) REVERT: A 395 VAL cc_start: 0.7557 (OUTLIER) cc_final: 0.7279 (p) REVERT: A 423 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6361 (p0) REVERT: A 477 LEU cc_start: 0.7161 (mm) cc_final: 0.6622 (mt) REVERT: B 8 ARG cc_start: 0.6424 (ttp-110) cc_final: 0.6029 (ttp80) REVERT: B 21 MET cc_start: 0.6476 (mmp) cc_final: 0.6137 (mmm) REVERT: B 102 PHE cc_start: 0.6548 (m-80) cc_final: 0.6274 (m-80) REVERT: B 188 ILE cc_start: 0.7192 (mm) cc_final: 0.6821 (pt) REVERT: B 201 TRP cc_start: 0.6511 (t60) cc_final: 0.6040 (t60) REVERT: B 277 ARG cc_start: 0.4899 (OUTLIER) cc_final: 0.3379 (mtm-85) REVERT: B 288 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6245 (tp) REVERT: B 293 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6654 (pp) REVERT: B 294 LEU cc_start: 0.7800 (mt) cc_final: 0.7389 (mp) REVERT: B 343 SER cc_start: 0.7077 (t) cc_final: 0.6588 (m) REVERT: B 373 LYS cc_start: 0.6074 (tttm) cc_final: 0.5814 (tttm) REVERT: B 382 TYR cc_start: 0.5139 (m-80) cc_final: 0.3949 (m-80) REVERT: B 391 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6973 (tp) REVERT: B 423 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6626 (p0) REVERT: B 453 ASN cc_start: 0.7228 (t0) cc_final: 0.6766 (t0) REVERT: C 8 ARG cc_start: 0.6391 (ttp-110) cc_final: 0.6119 (ttp80) REVERT: C 103 PHE cc_start: 0.6875 (t80) cc_final: 0.6583 (t80) REVERT: C 201 TRP cc_start: 0.6188 (t60) cc_final: 0.5928 (t60) REVERT: C 271 TRP cc_start: 0.7389 (t-100) cc_final: 0.6751 (t-100) REVERT: C 294 LEU cc_start: 0.7660 (mt) cc_final: 0.7262 (mp) REVERT: C 356 MET cc_start: 0.8079 (ptp) cc_final: 0.7763 (ptm) REVERT: C 363 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6635 (tt) REVERT: C 373 LYS cc_start: 0.7004 (mtpp) cc_final: 0.6596 (tttt) REVERT: C 382 TYR cc_start: 0.5208 (m-80) cc_final: 0.4537 (m-80) REVERT: C 457 LYS cc_start: 0.7909 (mttt) cc_final: 0.7634 (mttt) REVERT: C 469 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6336 (pt) REVERT: D 21 MET cc_start: 0.6544 (mmp) cc_final: 0.6328 (mmm) REVERT: D 103 PHE cc_start: 0.6658 (t80) cc_final: 0.6395 (t80) REVERT: D 205 MET cc_start: 0.4117 (pmm) cc_final: 0.3601 (ptp) REVERT: D 280 ILE cc_start: 0.7768 (mm) cc_final: 0.7522 (mp) REVERT: D 288 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6239 (tp) REVERT: D 294 LEU cc_start: 0.7668 (mt) cc_final: 0.7280 (mp) REVERT: D 358 VAL cc_start: 0.6972 (t) cc_final: 0.6635 (p) REVERT: D 361 ILE cc_start: 0.5970 (OUTLIER) cc_final: 0.5560 (tt) REVERT: D 362 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.5678 (mp) REVERT: D 370 ARG cc_start: 0.6617 (ttt180) cc_final: 0.6003 (ptt180) REVERT: D 382 TYR cc_start: 0.5310 (m-80) cc_final: 0.4146 (m-80) REVERT: D 447 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5765 (mp) REVERT: D 471 ILE cc_start: 0.7007 (pt) cc_final: 0.6805 (mp) REVERT: D 477 LEU cc_start: 0.7407 (mm) cc_final: 0.7102 (mt) REVERT: E 247 LEU cc_start: 0.6785 (tp) cc_final: 0.6107 (pp) REVERT: E 270 LEU cc_start: 0.5525 (tt) cc_final: 0.5103 (pp) REVERT: E 300 VAL cc_start: 0.6300 (p) cc_final: 0.5907 (t) REVERT: F 56 ASP cc_start: 0.0177 (OUTLIER) cc_final: -0.0343 (p0) REVERT: F 91 ASN cc_start: 0.4926 (t0) cc_final: 0.4504 (m-40) REVERT: F 247 LEU cc_start: 0.6632 (tp) cc_final: 0.6159 (pp) REVERT: F 249 LYS cc_start: 0.5433 (mttm) cc_final: 0.5002 (pttt) REVERT: F 293 GLU cc_start: 0.4578 (mm-30) cc_final: 0.4308 (mp0) REVERT: F 302 ILE cc_start: 0.6600 (mt) cc_final: 0.6317 (mm) REVERT: G 56 ASP cc_start: 0.0230 (OUTLIER) cc_final: -0.0107 (p0) REVERT: G 247 LEU cc_start: 0.7038 (tp) cc_final: 0.6330 (pp) REVERT: G 292 GLU cc_start: 0.4976 (tt0) cc_final: 0.4543 (tp30) REVERT: G 308 ASP cc_start: 0.3696 (OUTLIER) cc_final: 0.3138 (t0) REVERT: H 56 ASP cc_start: 0.0091 (OUTLIER) cc_final: -0.0228 (p0) REVERT: H 243 ILE cc_start: 0.7635 (mt) cc_final: 0.7163 (tt) REVERT: H 247 LEU cc_start: 0.6413 (tp) cc_final: 0.5995 (pp) REVERT: H 249 LYS cc_start: 0.5123 (mttp) cc_final: 0.4783 (pttt) REVERT: H 259 LEU cc_start: 0.5184 (tp) cc_final: 0.4800 (tm) REVERT: H 275 GLU cc_start: 0.5201 (mt-10) cc_final: 0.4493 (mm-30) REVERT: H 292 GLU cc_start: 0.4860 (tt0) cc_final: 0.4480 (pt0) REVERT: H 327 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5610 (tmt) outliers start: 95 outliers final: 62 residues processed: 457 average time/residue: 0.8955 time to fit residues: 482.8401 Evaluate side-chains 470 residues out of total 2193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 388 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 TYR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain E residue 242 ASN Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 308 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 327 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 26 optimal weight: 0.0570 chunk 38 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 313 GLN B 213 HIS B 313 GLN B 448 HIS C 213 HIS C 453 ASN D 213 HIS ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.236161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.226043 restraints weight = 31856.965| |-----------------------------------------------------------------------------| r_work (start): 0.4648 rms_B_bonded: 0.88 r_work: 0.4577 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.4513 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.4513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5258 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21078 Z= 0.192 Angle : 0.722 13.908 28651 Z= 0.349 Chirality : 0.043 0.226 3441 Planarity : 0.004 0.070 3553 Dihedral : 5.545 55.188 2822 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.17 % Allowed : 25.36 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.15), residues: 2623 helix: -0.27 (0.13), residues: 1390 sheet: 0.82 (0.42), residues: 156 loop : -2.01 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 54 HIS 0.004 0.001 HIS D 448 PHE 0.036 0.002 PHE B 281 TYR 0.034 0.002 TYR B 304 ARG 0.006 0.000 ARG D 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7705.43 seconds wall clock time: 136 minutes 46.79 seconds (8206.79 seconds total)