Starting phenix.real_space_refine on Sat Apr 6 07:31:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqn_40711/04_2024/8sqn_40711.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqn_40711/04_2024/8sqn_40711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqn_40711/04_2024/8sqn_40711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqn_40711/04_2024/8sqn_40711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqn_40711/04_2024/8sqn_40711.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqn_40711/04_2024/8sqn_40711.pdb" } resolution = 3.89 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 176 5.16 5 C 18053 2.51 5 N 4916 2.21 5 O 5352 1.98 5 H 27807 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 97": "OD1" <-> "OD2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B ASP 284": "OD1" <-> "OD2" Residue "B ASP 311": "OD1" <-> "OD2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 385": "OD1" <-> "OD2" Residue "D ASP 39": "OD1" <-> "OD2" Residue "D TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D ASP 350": "OD1" <-> "OD2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 117": "OD1" <-> "OD2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 264": "OE1" <-> "OE2" Residue "F ASP 305": "OD1" <-> "OD2" Residue "F GLU 390": "OE1" <-> "OE2" Residue "H TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 42": "OD1" <-> "OD2" Residue "H PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H ASP 308": "OD1" <-> "OD2" Residue "J GLU 30": "OE1" <-> "OE2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 145": "OD1" <-> "OD2" Residue "J ASP 158": "OD1" <-> "OD2" Residue "J TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 188": "OD1" <-> "OD2" Residue "J ASP 218": "OD1" <-> "OD2" Residue "J GLU 264": "OE1" <-> "OE2" Residue "J ASP 281": "OD1" <-> "OD2" Residue "J PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 390": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "N TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 97": "OD1" <-> "OD2" Residue "N ASP 113": "OD1" <-> "OD2" Residue "N TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 191": "OE1" <-> "OE2" Residue "N TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 241": "OE1" <-> "OE2" Residue "N ASP 281": "OD1" <-> "OD2" Residue "N ASP 284": "OD1" <-> "OD2" Residue "N ASP 385": "OD1" <-> "OD2" Residue "P GLU 35": "OE1" <-> "OE2" Residue "P GLU 40": "OE1" <-> "OE2" Residue "P TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 141": "OE1" <-> "OE2" Residue "P ASP 245": "OD1" <-> "OD2" Residue "P GLU 312": "OE1" <-> "OE2" Residue "P PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 327": "OE1" <-> "OE2" Residue "P GLU 330": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 56304 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4190 Classifications: {'peptide': 265} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 257} Chain: "B" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6568 Classifications: {'peptide': 438} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 410} Chain: "D" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6429 Classifications: {'peptide': 415} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "F" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6568 Classifications: {'peptide': 438} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 410} Chain: "H" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6429 Classifications: {'peptide': 415} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "J" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6568 Classifications: {'peptide': 438} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain: "L" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6429 Classifications: {'peptide': 415} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "N" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6568 Classifications: {'peptide': 438} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 410} Chain: "P" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6429 Classifications: {'peptide': 415} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 18.51, per 1000 atoms: 0.33 Number of scatterers: 56304 At special positions: 0 Unit cell: (194.4, 163.2, 210, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 176 16.00 O 5352 8.00 N 4916 7.00 C 18053 6.00 H 27807 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 78 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.04 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.04 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.06 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 28 " distance=2.03 Simple disulfide: pdb=" SG CYS D 94 " - pdb=" SG CYS D 108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 155 " - pdb=" SG CYS D 269 " distance=2.03 Simple disulfide: pdb=" SG CYS D 204 " - pdb=" SG CYS D 229 " distance=2.03 Simple disulfide: pdb=" SG CYS D 206 " - pdb=" SG CYS D 223 " distance=2.04 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 68 " - pdb=" SG CYS F 78 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 271 " distance=2.03 Simple disulfide: pdb=" SG CYS F 301 " - pdb=" SG CYS F 376 " distance=2.03 Simple disulfide: pdb=" SG CYS F 306 " - pdb=" SG CYS F 380 " distance=2.03 Simple disulfide: pdb=" SG CYS F 328 " - pdb=" SG CYS F 370 " distance=2.04 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 127 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 28 " distance=2.03 Simple disulfide: pdb=" SG CYS H 94 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 269 " distance=2.03 Simple disulfide: pdb=" SG CYS H 204 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS H 206 " - pdb=" SG CYS H 223 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.04 Simple disulfide: pdb=" SG CYS J 301 " - pdb=" SG CYS J 376 " distance=2.04 Simple disulfide: pdb=" SG CYS J 306 " - pdb=" SG CYS J 380 " distance=2.03 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.04 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 127 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 28 " distance=2.03 Simple disulfide: pdb=" SG CYS L 94 " - pdb=" SG CYS L 108 " distance=2.03 Simple disulfide: pdb=" SG CYS L 155 " - pdb=" SG CYS L 269 " distance=2.03 Simple disulfide: pdb=" SG CYS L 204 " - pdb=" SG CYS L 229 " distance=2.04 Simple disulfide: pdb=" SG CYS L 206 " - pdb=" SG CYS L 223 " distance=2.04 Simple disulfide: pdb=" SG CYS N 49 " - pdb=" SG CYS N 114 " distance=2.03 Simple disulfide: pdb=" SG CYS N 62 " - pdb=" SG CYS N 94 " distance=2.03 Simple disulfide: pdb=" SG CYS N 63 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 68 " - pdb=" SG CYS N 78 " distance=2.03 Simple disulfide: pdb=" SG CYS N 259 " - pdb=" SG CYS N 271 " distance=2.04 Simple disulfide: pdb=" SG CYS N 301 " - pdb=" SG CYS N 376 " distance=2.04 Simple disulfide: pdb=" SG CYS N 306 " - pdb=" SG CYS N 380 " distance=2.03 Simple disulfide: pdb=" SG CYS N 328 " - pdb=" SG CYS N 370 " distance=2.03 Simple disulfide: pdb=" SG CYS P 19 " - pdb=" SG CYS P 127 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 28 " distance=2.05 Simple disulfide: pdb=" SG CYS P 94 " - pdb=" SG CYS P 108 " distance=2.03 Simple disulfide: pdb=" SG CYS P 155 " - pdb=" SG CYS P 269 " distance=2.03 Simple disulfide: pdb=" SG CYS P 204 " - pdb=" SG CYS P 229 " distance=2.03 Simple disulfide: pdb=" SG CYS P 206 " - pdb=" SG CYS P 223 " 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 Links applied NAG-ASN " NAG B 501 " - " ASN B 139 " " NAG D 501 " - " ASN D 199 " " NAG F 501 " - " ASN F 139 " " NAG H 501 " - " ASN H 199 " " NAG J 501 " - " ASN J 139 " " NAG L 501 " - " ASN L 199 " " NAG N 501 " - " ASN N 139 " " NAG P 501 " - " ASN P 199 " Time building additional restraints: 33.24 Conformation dependent library (CDL) restraints added in 4.5 seconds 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6860 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 82 sheets defined 14.1% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.528A pdb=" N ALA A 164 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 237 through 243 Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.538A pdb=" N GLU A 268 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.827A pdb=" N GLY B 258 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 259' Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 403 through 414 Processing helix chain 'B' and resid 416 through 438 removed outlier: 3.596A pdb=" N LEU B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 357 through 365 removed outlier: 4.363A pdb=" N HIS D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 400 removed outlier: 3.570A pdb=" N VAL D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 372 " --> pdb=" O VAL D 368 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 373 " --> pdb=" O TYR D 369 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU D 374 " --> pdb=" O THR D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 419 Processing helix chain 'F' and resid 113 through 118 Processing helix chain 'F' and resid 238 through 247 removed outlier: 3.602A pdb=" N MET F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 254 removed outlier: 3.648A pdb=" N GLU F 253 " --> pdb=" O PRO F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.830A pdb=" N GLY F 258 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS F 259 " --> pdb=" O PRO F 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 255 through 259' Processing helix chain 'F' and resid 283 through 287 Processing helix chain 'F' and resid 403 through 414 Processing helix chain 'F' and resid 416 through 438 Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 225 through 227 No H-bonds generated for 'chain 'H' and resid 225 through 227' Processing helix chain 'H' and resid 357 through 365 removed outlier: 4.322A pdb=" N HIS H 361 " --> pdb=" O GLU H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 401 removed outlier: 3.565A pdb=" N VAL H 371 " --> pdb=" O PRO H 367 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE H 372 " --> pdb=" O VAL H 368 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL H 373 " --> pdb=" O TYR H 369 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU H 374 " --> pdb=" O THR H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 419 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 238 through 246 Processing helix chain 'J' and resid 255 through 259 removed outlier: 3.635A pdb=" N GLY J 258 " --> pdb=" O ALA J 255 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS J 259 " --> pdb=" O PRO J 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 255 through 259' Processing helix chain 'J' and resid 403 through 414 removed outlier: 3.579A pdb=" N PHE J 414 " --> pdb=" O LEU J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 438 Processing helix chain 'L' and resid 358 through 365 removed outlier: 3.639A pdb=" N TYR L 362 " --> pdb=" O ILE L 358 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 401 removed outlier: 3.710A pdb=" N VAL L 371 " --> pdb=" O PRO L 367 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE L 372 " --> pdb=" O VAL L 368 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL L 373 " --> pdb=" O TYR L 369 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU L 374 " --> pdb=" O THR L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 419 Processing helix chain 'N' and resid 113 through 118 Processing helix chain 'N' and resid 238 through 246 Processing helix chain 'N' and resid 250 through 254 removed outlier: 3.804A pdb=" N GLU N 253 " --> pdb=" O PRO N 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 255 through 259 removed outlier: 3.733A pdb=" N GLY N 258 " --> pdb=" O ALA N 255 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS N 259 " --> pdb=" O PRO N 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 255 through 259' Processing helix chain 'N' and resid 283 through 287 Processing helix chain 'N' and resid 403 through 414 removed outlier: 3.555A pdb=" N PHE N 414 " --> pdb=" O LEU N 410 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 438 removed outlier: 3.910A pdb=" N LEU N 420 " --> pdb=" O GLY N 416 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 84 No H-bonds generated for 'chain 'P' and resid 82 through 84' Processing helix chain 'P' and resid 225 through 227 No H-bonds generated for 'chain 'P' and resid 225 through 227' Processing helix chain 'P' and resid 357 through 365 removed outlier: 4.314A pdb=" N HIS P 361 " --> pdb=" O GLU P 357 " (cutoff:3.500A) Processing helix chain 'P' and resid 366 through 400 removed outlier: 3.577A pdb=" N VAL P 371 " --> pdb=" O PRO P 367 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE P 372 " --> pdb=" O VAL P 368 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL P 373 " --> pdb=" O TYR P 369 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU P 374 " --> pdb=" O THR P 370 " (cutoff:3.500A) Processing helix chain 'P' and resid 411 through 419 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 44 removed outlier: 6.780A pdb=" N VAL A 206 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP A 225 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP A 208 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP A 221 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 93 removed outlier: 6.805A pdb=" N TRP A 74 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASP A 91 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 72 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR A 93 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG A 70 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 10.678A pdb=" N ALA A 173 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LYS A 152 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ILE A 175 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN A 154 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA A 177 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP A 156 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 8 removed outlier: 3.687A pdb=" N ILE B 162 " --> pdb=" O SER B 279 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 17 removed outlier: 5.571A pdb=" N ILE B 31 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL B 136 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL B 33 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG B 134 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B 35 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B 41 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N THR B 126 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASN B 43 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL B 124 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU B 45 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU B 122 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 47 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 120 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 140 through 147 removed outlier: 6.750A pdb=" N VAL B 120 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 47 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU B 122 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU B 45 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL B 124 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASN B 43 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N THR B 126 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER B 41 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B 35 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG B 134 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL B 33 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL B 136 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE B 31 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AB1, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AB3, first strand: chain 'B' and resid 219 through 221 Processing sheet with id=AB4, first strand: chain 'B' and resid 296 through 302 removed outlier: 4.186A pdb=" N VAL B 299 " --> pdb=" O GLN B 319 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN B 319 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS B 301 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR B 317 " --> pdb=" O CYS B 301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 343 through 346 removed outlier: 3.673A pdb=" N GLY B 326 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 387 through 388 removed outlier: 5.865A pdb=" N GLU D 337 " --> pdb=" O TRP D 333 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TRP D 333 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 17 through 19 Processing sheet with id=AB8, first strand: chain 'D' and resid 34 through 38 removed outlier: 4.343A pdb=" N ASN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.203A pdb=" N TYR D 69 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 86 through 89 Processing sheet with id=AC2, first strand: chain 'D' and resid 151 through 158 Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 171 Processing sheet with id=AC4, first strand: chain 'D' and resid 183 through 184 Processing sheet with id=AC5, first strand: chain 'D' and resid 210 through 215 Processing sheet with id=AC6, first strand: chain 'D' and resid 278 through 279 removed outlier: 3.897A pdb=" N THR D 278 " --> pdb=" O HIS D 289 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 2 through 8 Processing sheet with id=AC8, first strand: chain 'F' and resid 15 through 21 removed outlier: 3.622A pdb=" N VAL F 19 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 27 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG F 21 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ALA F 25 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLU F 30 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR F 137 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR F 32 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE F 135 " --> pdb=" O THR F 32 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL F 34 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU F 133 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N SER F 36 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL F 131 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU F 38 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F 129 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA F 127 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR F 42 " --> pdb=" O HIS F 125 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS F 125 " --> pdb=" O THR F 42 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS F 44 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS F 123 " --> pdb=" O LYS F 44 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR F 46 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 140 through 147 removed outlier: 3.629A pdb=" N TYR F 46 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS F 123 " --> pdb=" O LYS F 44 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS F 44 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS F 125 " --> pdb=" O THR F 42 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR F 42 " --> pdb=" O HIS F 125 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA F 127 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F 129 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU F 38 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL F 131 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N SER F 36 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU F 133 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL F 34 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE F 135 " --> pdb=" O THR F 32 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR F 32 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR F 137 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLU F 30 " --> pdb=" O TYR F 137 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 51 through 54 Processing sheet with id=AD2, first strand: chain 'F' and resid 51 through 54 Processing sheet with id=AD3, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AD4, first strand: chain 'F' and resid 219 through 221 Processing sheet with id=AD5, first strand: chain 'F' and resid 296 through 302 removed outlier: 4.115A pdb=" N VAL F 299 " --> pdb=" O GLN F 319 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN F 319 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS F 301 " --> pdb=" O THR F 317 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR F 317 " --> pdb=" O CYS F 301 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 343 through 346 removed outlier: 3.748A pdb=" N GLY F 326 " --> pdb=" O VAL F 346 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 387 through 388 Processing sheet with id=AD8, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=AD9, first strand: chain 'H' and resid 34 through 38 removed outlier: 4.309A pdb=" N ASN H 36 " --> pdb=" O GLN H 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN H 49 " --> pdb=" O ASN H 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.692A pdb=" N GLY H 55 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR H 69 " --> pdb=" O GLY H 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 86 through 89 Processing sheet with id=AE3, first strand: chain 'H' and resid 151 through 158 Processing sheet with id=AE4, first strand: chain 'H' and resid 240 through 241 Processing sheet with id=AE5, first strand: chain 'H' and resid 183 through 184 Processing sheet with id=AE6, first strand: chain 'H' and resid 210 through 215 Processing sheet with id=AE7, first strand: chain 'H' and resid 286 through 291 Processing sheet with id=AE8, first strand: chain 'H' and resid 296 through 300 Processing sheet with id=AE9, first strand: chain 'J' and resid 2 through 8 removed outlier: 3.581A pdb=" N ILE J 162 " --> pdb=" O SER J 279 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP J 281 " --> pdb=" O LYS J 160 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LYS J 160 " --> pdb=" O ASP J 281 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 15 through 17 removed outlier: 5.591A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER J 35 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU J 45 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL J 47 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 140 through 147 removed outlier: 6.672A pdb=" N VAL J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL J 47 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU J 45 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER J 35 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 51 through 54 Processing sheet with id=AF4, first strand: chain 'J' and resid 51 through 54 Processing sheet with id=AF5, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=AF6, first strand: chain 'J' and resid 220 through 221 Processing sheet with id=AF7, first strand: chain 'J' and resid 296 through 302 removed outlier: 4.064A pdb=" N VAL J 299 " --> pdb=" O GLN J 319 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN J 319 " --> pdb=" O VAL J 299 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N CYS J 301 " --> pdb=" O THR J 317 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR J 317 " --> pdb=" O CYS J 301 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 343 through 346 removed outlier: 3.628A pdb=" N GLY J 326 " --> pdb=" O VAL J 346 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 387 through 388 removed outlier: 5.823A pdb=" N GLU L 337 " --> pdb=" O TRP L 333 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TRP L 333 " --> pdb=" O GLU L 337 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 17 through 19 Processing sheet with id=AG2, first strand: chain 'L' and resid 34 through 38 removed outlier: 4.273A pdb=" N ASN L 36 " --> pdb=" O GLN L 49 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN L 107 " --> pdb=" O ARG L 96 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ARG L 96 " --> pdb=" O GLN L 107 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AG4, first strand: chain 'L' and resid 86 through 89 Processing sheet with id=AG5, first strand: chain 'L' and resid 151 through 158 Processing sheet with id=AG6, first strand: chain 'L' and resid 169 through 171 Processing sheet with id=AG7, first strand: chain 'L' and resid 183 through 184 Processing sheet with id=AG8, first strand: chain 'L' and resid 210 through 215 Processing sheet with id=AG9, first strand: chain 'L' and resid 278 through 279 removed outlier: 3.821A pdb=" N THR L 278 " --> pdb=" O HIS L 289 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 2 through 8 removed outlier: 4.474A pdb=" N ASP N 281 " --> pdb=" O LYS N 160 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS N 160 " --> pdb=" O ASP N 281 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL N 161 " --> pdb=" O GLY N 154 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 15 through 21 removed outlier: 3.601A pdb=" N VAL N 19 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU N 27 " --> pdb=" O VAL N 19 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ARG N 21 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ALA N 25 " --> pdb=" O ARG N 21 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE N 31 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL N 136 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL N 33 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG N 134 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER N 35 " --> pdb=" O GLY N 132 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY N 132 " --> pdb=" O SER N 35 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER N 41 " --> pdb=" O THR N 126 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR N 126 " --> pdb=" O SER N 41 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASN N 43 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL N 124 " --> pdb=" O ASN N 43 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU N 45 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU N 122 " --> pdb=" O GLU N 45 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL N 47 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL N 120 " --> pdb=" O VAL N 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 140 through 147 removed outlier: 6.750A pdb=" N VAL N 120 " --> pdb=" O VAL N 47 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL N 47 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU N 122 " --> pdb=" O GLU N 45 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU N 45 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL N 124 " --> pdb=" O ASN N 43 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASN N 43 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR N 126 " --> pdb=" O SER N 41 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER N 41 " --> pdb=" O THR N 126 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY N 132 " --> pdb=" O SER N 35 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER N 35 " --> pdb=" O GLY N 132 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG N 134 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL N 33 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL N 136 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE N 31 " --> pdb=" O VAL N 136 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 51 through 54 removed outlier: 3.528A pdb=" N TYR N 107 " --> pdb=" O VAL N 54 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'N' and resid 51 through 54 removed outlier: 3.528A pdb=" N TYR N 107 " --> pdb=" O VAL N 54 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'N' and resid 203 through 204 removed outlier: 3.641A pdb=" N GLN N 204 " --> pdb=" O VAL N 214 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL N 214 " --> pdb=" O GLN N 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'N' and resid 220 through 221 Processing sheet with id=AH8, first strand: chain 'N' and resid 296 through 302 removed outlier: 4.099A pdb=" N VAL N 299 " --> pdb=" O GLN N 319 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN N 319 " --> pdb=" O VAL N 299 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS N 301 " --> pdb=" O THR N 317 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR N 317 " --> pdb=" O CYS N 301 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 343 through 346 removed outlier: 3.714A pdb=" N GLY N 326 " --> pdb=" O VAL N 346 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'N' and resid 387 through 388 Processing sheet with id=AI2, first strand: chain 'P' and resid 17 through 19 Processing sheet with id=AI3, first strand: chain 'P' and resid 37 through 38 removed outlier: 10.563A pdb=" N SER P 51 " --> pdb=" O ASP P 73 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP P 73 " --> pdb=" O SER P 51 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N TYR P 69 " --> pdb=" O GLY P 55 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'P' and resid 37 through 38 removed outlier: 11.264A pdb=" N ILE P 48 " --> pdb=" O GLN P 107 " (cutoff:3.500A) removed outlier: 10.550A pdb=" N GLN P 107 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N VAL P 50 " --> pdb=" O LEU P 105 " (cutoff:3.500A) removed outlier: 10.471A pdb=" N LEU P 105 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N ALA P 52 " --> pdb=" O PHE P 103 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE P 103 " --> pdb=" O ALA P 52 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR P 56 " --> pdb=" O HIS P 99 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N HIS P 99 " --> pdb=" O TYR P 56 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE P 88 " --> pdb=" O CYS P 94 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG P 96 " --> pdb=" O LEU P 86 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N LEU P 86 " --> pdb=" O ARG P 96 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'P' and resid 151 through 158 Processing sheet with id=AI6, first strand: chain 'P' and resid 169 through 171 Processing sheet with id=AI7, first strand: chain 'P' and resid 183 through 184 Processing sheet with id=AI8, first strand: chain 'P' and resid 210 through 215 Processing sheet with id=AI9, first strand: chain 'P' and resid 286 through 290 Processing sheet with id=AJ1, first strand: chain 'P' and resid 296 through 300 1016 hydrogen bonds defined for protein. 2607 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: 18.32 Time building geometry restraints manager: 35.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 27806 1.04 - 1.24: 3885 1.24 - 1.45: 8859 1.45 - 1.65: 16287 1.65 - 1.85: 214 Bond restraints: 57051 Sorted by residual: bond pdb=" N PHE B 1 " pdb=" H3 PHE B 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N ILE L 5 " pdb=" H3 ILE L 5 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N ILE H 5 " pdb=" H2 ILE H 5 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N ILE P 5 " pdb=" H2 ILE P 5 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N PHE N 1 " pdb=" H3 PHE N 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 57046 not shown) Histogram of bond angle deviations from ideal: 4.38 - 30.65: 4 30.65 - 56.91: 0 56.91 - 83.17: 14 83.17 - 109.44: 37602 109.44 - 135.70: 65506 Bond angle restraints: 103126 Sorted by residual: angle pdb=" H1 ILE H 5 " pdb=" N ILE H 5 " pdb=" H2 ILE H 5 " ideal model delta sigma weight residual 109.47 4.38 105.09 3.00e+00 1.11e-01 1.23e+03 angle pdb=" H1 ILE L 5 " pdb=" N ILE L 5 " pdb=" H2 ILE L 5 " ideal model delta sigma weight residual 109.47 4.47 105.00 3.00e+00 1.11e-01 1.22e+03 angle pdb=" H1 ILE D 5 " pdb=" N ILE D 5 " pdb=" H2 ILE D 5 " ideal model delta sigma weight residual 109.47 7.85 101.62 3.00e+00 1.11e-01 1.15e+03 angle pdb=" H1 ILE P 5 " pdb=" N ILE P 5 " pdb=" H2 ILE P 5 " ideal model delta sigma weight residual 109.47 11.04 98.43 3.00e+00 1.11e-01 1.08e+03 angle pdb=" CB LEU H 405 " pdb=" CA LEU H 405 " pdb=" HA LEU H 405 " ideal model delta sigma weight residual 109.00 73.59 35.41 3.00e+00 1.11e-01 1.39e+02 ... (remaining 103121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 24069 17.99 - 35.98: 2425 35.98 - 53.98: 799 53.98 - 71.97: 149 71.97 - 89.96: 37 Dihedral angle restraints: 27479 sinusoidal: 14798 harmonic: 12681 Sorted by residual: dihedral pdb=" CB CYS H 155 " pdb=" SG CYS H 155 " pdb=" SG CYS H 269 " pdb=" CB CYS H 269 " ideal model delta sinusoidal sigma weight residual -86.00 -164.66 78.66 1 1.00e+01 1.00e-02 7.71e+01 dihedral pdb=" CB CYS B 328 " pdb=" SG CYS B 328 " pdb=" SG CYS B 370 " pdb=" CB CYS B 370 " ideal model delta sinusoidal sigma weight residual -86.00 -7.42 -78.58 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS P 22 " pdb=" SG CYS P 22 " pdb=" SG CYS P 28 " pdb=" CB CYS P 28 " ideal model delta sinusoidal sigma weight residual 93.00 17.82 75.18 1 1.00e+01 1.00e-02 7.14e+01 ... (remaining 27476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4073 0.078 - 0.156: 451 0.156 - 0.234: 1 0.234 - 0.312: 1 0.312 - 0.390: 4 Chirality restraints: 4530 Sorted by residual: chirality pdb=" CA LEU L 405 " pdb=" N LEU L 405 " pdb=" C LEU L 405 " pdb=" CB LEU L 405 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA LEU P 405 " pdb=" N LEU P 405 " pdb=" C LEU P 405 " pdb=" CB LEU P 405 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA LEU H 405 " pdb=" N LEU H 405 " pdb=" C LEU H 405 " pdb=" CB LEU H 405 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 4527 not shown) Planarity restraints: 8542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 264 " -0.116 5.00e-02 4.00e+02 1.67e-01 4.49e+01 pdb=" N PRO F 265 " 0.289 5.00e-02 4.00e+02 pdb=" CA PRO F 265 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO F 265 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 152 " -0.067 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO J 153 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO J 153 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO J 153 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 85 " -0.055 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO F 86 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO F 86 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 86 " -0.046 5.00e-02 4.00e+02 ... (remaining 8539 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 1865 2.13 - 2.75: 102550 2.75 - 3.37: 154288 3.37 - 3.98: 191789 3.98 - 4.60: 291620 Nonbonded interactions: 742112 Sorted by model distance: nonbonded pdb=" OE1 GLU F 264 " pdb=" H GLU F 264 " model vdw 1.518 1.850 nonbonded pdb=" OE1 GLU L 327 " pdb=" H GLU L 327 " model vdw 1.521 1.850 nonbonded pdb=" OE1 GLU J 390 " pdb=" H GLU J 390 " model vdw 1.522 1.850 nonbonded pdb="HH12 ARG D 47 " pdb=" O PRO D 261 " model vdw 1.536 1.850 nonbonded pdb=" O LEU A 240 " pdb=" H VAL A 244 " model vdw 1.555 1.850 ... (remaining 742107 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 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.660 Extract box with map and model: 6.640 Check model and map are aligned: 0.630 Set scattering table: 0.400 Process input model: 131.530 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 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 : 0.003 0.170 29244 Z= 0.209 Angle : 0.605 14.629 39858 Z= 0.320 Chirality : 0.045 0.390 4530 Planarity : 0.005 0.167 5093 Dihedral : 15.801 88.657 10640 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.29 % Allowed : 23.09 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3659 helix: 2.32 (0.27), residues: 395 sheet: -0.92 (0.15), residues: 1210 loop : -1.06 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 282 HIS 0.008 0.001 HIS P 149 PHE 0.022 0.001 PHE J 95 TYR 0.019 0.001 TYR H 182 ARG 0.005 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 553 time to evaluate : 3.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 ASN cc_start: 0.8074 (p0) cc_final: 0.7794 (p0) REVERT: J 46 TYR cc_start: 0.8782 (p90) cc_final: 0.8347 (p90) REVERT: J 218 ASP cc_start: 0.7814 (t0) cc_final: 0.7527 (t0) REVERT: L 69 TYR cc_start: 0.6299 (m-10) cc_final: 0.5749 (m-10) REVERT: L 80 GLU cc_start: 0.5793 (tt0) cc_final: 0.5362 (tt0) outliers start: 9 outliers final: 7 residues processed: 559 average time/residue: 0.6937 time to fit residues: 620.3480 Evaluate side-chains 536 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 529 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain P residue 108 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 4.9990 chunk 274 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 93 optimal weight: 0.0970 chunk 185 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 328 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS ** B 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 HIS ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 HIS D 99 HIS ** D 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 HIS H 74 HIS H 249 HIS ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 321 ASN J 9 ASN ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 275 HIS ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 HIS ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 249 HIS ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 228 ASN ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 24 HIS P 149 HIS P 249 HIS ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 29244 Z= 0.361 Angle : 0.620 6.513 39858 Z= 0.329 Chirality : 0.047 0.394 4530 Planarity : 0.005 0.114 5093 Dihedral : 5.345 64.942 4190 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.39 % Allowed : 21.26 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 3659 helix: 2.17 (0.25), residues: 413 sheet: -1.25 (0.15), residues: 1229 loop : -1.21 (0.14), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 243 HIS 0.009 0.001 HIS D 172 PHE 0.017 0.002 PHE P 54 TYR 0.020 0.002 TYR H 21 ARG 0.004 0.000 ARG D 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 566 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7882 (tp) REVERT: B 377 ASN cc_start: 0.7924 (p0) cc_final: 0.7665 (p0) REVERT: D 220 MET cc_start: 0.5880 (mmp) cc_final: 0.5164 (mmt) REVERT: F 196 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.7945 (p0) REVERT: F 202 ASP cc_start: 0.7711 (p0) cc_final: 0.7235 (p0) REVERT: F 219 ILE cc_start: 0.8867 (mp) cc_final: 0.8633 (tt) REVERT: F 334 SER cc_start: 0.8242 (m) cc_final: 0.7780 (t) REVERT: H 61 THR cc_start: 0.2955 (OUTLIER) cc_final: 0.2254 (m) REVERT: H 234 ARG cc_start: 0.7241 (ptt90) cc_final: 0.6845 (ptt90) REVERT: H 248 ARG cc_start: 0.7599 (mtp180) cc_final: 0.7148 (mtp180) REVERT: H 366 HIS cc_start: 0.7180 (m170) cc_final: 0.6965 (m90) REVERT: J 352 ILE cc_start: 0.7718 (tt) cc_final: 0.7480 (mm) REVERT: L 69 TYR cc_start: 0.6753 (m-10) cc_final: 0.6031 (m-10) REVERT: L 80 GLU cc_start: 0.6137 (tt0) cc_final: 0.5835 (tt0) REVERT: N 387 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8090 (pt) REVERT: P 39 ASP cc_start: 0.7512 (p0) cc_final: 0.7272 (p0) outliers start: 106 outliers final: 66 residues processed: 630 average time/residue: 0.7426 time to fit residues: 755.1314 Evaluate side-chains 601 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 531 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 241 PHE Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 110 PHE Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 195 MET Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 318 THR Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 107 TYR Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 336 THR Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 367 VAL Chi-restraints excluded: chain N residue 387 ILE Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 149 HIS Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 300 THR Chi-restraints excluded: chain P residue 317 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 182 optimal weight: 1.9990 chunk 102 optimal weight: 0.0000 chunk 273 optimal weight: 6.9990 chunk 223 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 329 optimal weight: 1.9990 chunk 355 optimal weight: 4.9990 chunk 293 optimal weight: 0.9980 chunk 326 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 HIS ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29244 Z= 0.239 Angle : 0.570 6.437 39858 Z= 0.300 Chirality : 0.045 0.388 4530 Planarity : 0.004 0.094 5093 Dihedral : 5.136 65.767 4185 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.49 % Allowed : 21.55 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3659 helix: 2.17 (0.25), residues: 413 sheet: -1.24 (0.15), residues: 1228 loop : -1.19 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 243 HIS 0.027 0.001 HIS P 149 PHE 0.014 0.001 PHE J 95 TYR 0.020 0.001 TYR L 21 ARG 0.004 0.000 ARG D 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 549 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 CYS cc_start: 0.6595 (OUTLIER) cc_final: 0.6325 (p) REVERT: B 103 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7777 (tp) REVERT: B 241 GLU cc_start: 0.7608 (tp30) cc_final: 0.7217 (tm-30) REVERT: D 43 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7437 (t0) REVERT: D 220 MET cc_start: 0.5934 (mmp) cc_final: 0.5264 (mmt) REVERT: F 95 PHE cc_start: 0.6509 (p90) cc_final: 0.6227 (p90) REVERT: F 196 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8014 (p0) REVERT: F 202 ASP cc_start: 0.7824 (p0) cc_final: 0.7198 (p0) REVERT: F 219 ILE cc_start: 0.8863 (mp) cc_final: 0.8613 (tt) REVERT: F 334 SER cc_start: 0.8253 (m) cc_final: 0.7795 (t) REVERT: H 21 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.7150 (m-80) REVERT: H 61 THR cc_start: 0.2869 (OUTLIER) cc_final: 0.1794 (m) REVERT: H 234 ARG cc_start: 0.7248 (ptt90) cc_final: 0.6875 (ptt90) REVERT: J 278 ILE cc_start: 0.8743 (tt) cc_final: 0.8500 (pt) REVERT: J 352 ILE cc_start: 0.7863 (tt) cc_final: 0.7616 (mm) REVERT: J 373 LYS cc_start: 0.7325 (mttm) cc_final: 0.7026 (mttp) REVERT: L 69 TYR cc_start: 0.6827 (m-10) cc_final: 0.6130 (m-10) REVERT: L 80 GLU cc_start: 0.6246 (tt0) cc_final: 0.6036 (tt0) REVERT: L 115 THR cc_start: 0.8589 (m) cc_final: 0.8386 (t) REVERT: P 149 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7706 (p-80) outliers start: 109 outliers final: 74 residues processed: 623 average time/residue: 0.6888 time to fit residues: 683.1792 Evaluate side-chains 616 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 535 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 118 HIS Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 110 PHE Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 145 ASP Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 318 THR Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain L residue 345 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 367 VAL Chi-restraints excluded: chain N residue 370 CYS Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 149 HIS Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 317 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 325 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 330 optimal weight: 1.9990 chunk 349 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 313 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 HIS ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 HIS ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 149 HIS ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29244 Z= 0.273 Angle : 0.572 6.380 39858 Z= 0.301 Chirality : 0.045 0.390 4530 Planarity : 0.005 0.094 5093 Dihedral : 5.142 66.345 4185 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.58 % Allowed : 21.33 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3659 helix: 2.22 (0.25), residues: 413 sheet: -1.27 (0.15), residues: 1228 loop : -1.25 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 243 HIS 0.009 0.001 HIS H 366 PHE 0.020 0.001 PHE N 87 TYR 0.019 0.001 TYR H 21 ARG 0.005 0.000 ARG H 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 556 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 CYS cc_start: 0.6605 (OUTLIER) cc_final: 0.6218 (p) REVERT: B 47 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8964 (m) REVERT: B 103 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7747 (tp) REVERT: B 131 VAL cc_start: 0.9206 (t) cc_final: 0.8981 (m) REVERT: B 188 ASP cc_start: 0.6742 (t0) cc_final: 0.6526 (t0) REVERT: B 270 ASN cc_start: 0.8193 (t0) cc_final: 0.7403 (t0) REVERT: D 43 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7692 (t0) REVERT: D 80 GLU cc_start: 0.7582 (pm20) cc_final: 0.7287 (pm20) REVERT: D 220 MET cc_start: 0.6151 (mmp) cc_final: 0.5554 (mmt) REVERT: D 327 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7773 (pm20) REVERT: F 117 ASP cc_start: 0.8094 (t0) cc_final: 0.7771 (t0) REVERT: F 196 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.7979 (p0) REVERT: F 202 ASP cc_start: 0.7977 (p0) cc_final: 0.7259 (p0) REVERT: F 219 ILE cc_start: 0.8882 (mp) cc_final: 0.8672 (tt) REVERT: F 334 SER cc_start: 0.8312 (m) cc_final: 0.7903 (t) REVERT: H 21 TYR cc_start: 0.7423 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: H 61 THR cc_start: 0.2868 (OUTLIER) cc_final: 0.1769 (m) REVERT: H 234 ARG cc_start: 0.7257 (ptt90) cc_final: 0.6883 (ptt90) REVERT: H 255 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.5680 (mp10) REVERT: J 46 TYR cc_start: 0.9004 (p90) cc_final: 0.8652 (p90) REVERT: J 352 ILE cc_start: 0.8022 (tt) cc_final: 0.7709 (mm) REVERT: L 69 TYR cc_start: 0.6976 (m-10) cc_final: 0.6202 (m-10) REVERT: L 80 GLU cc_start: 0.5987 (tt0) cc_final: 0.5531 (tt0) REVERT: N 75 ASP cc_start: 0.8309 (t0) cc_final: 0.7602 (t0) outliers start: 143 outliers final: 103 residues processed: 647 average time/residue: 0.6967 time to fit residues: 714.3264 Evaluate side-chains 636 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 524 time to evaluate : 3.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 118 HIS Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain H residue 255 GLN Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 110 PHE Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 228 ASN Chi-restraints excluded: chain J residue 238 SER Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 321 LYS Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 70 MET Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain L residue 263 ARG Chi-restraints excluded: chain L residue 318 THR Chi-restraints excluded: chain L residue 345 GLU Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 280 ILE Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 367 VAL Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 149 HIS Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 265 THR Chi-restraints excluded: chain P residue 300 THR Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain P residue 345 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 291 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 260 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 178 optimal weight: 0.9990 chunk 314 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29244 Z= 0.207 Angle : 0.555 6.502 39858 Z= 0.290 Chirality : 0.045 0.387 4530 Planarity : 0.004 0.075 5093 Dihedral : 4.994 67.120 4184 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.71 % Allowed : 22.16 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3659 helix: 2.32 (0.25), residues: 413 sheet: -1.22 (0.15), residues: 1228 loop : -1.18 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 243 HIS 0.032 0.001 HIS P 149 PHE 0.034 0.001 PHE F 95 TYR 0.018 0.001 TYR L 21 ARG 0.003 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 540 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 CYS cc_start: 0.6451 (OUTLIER) cc_final: 0.6239 (p) REVERT: B 47 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8972 (m) REVERT: B 103 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7706 (tp) REVERT: B 131 VAL cc_start: 0.9210 (t) cc_final: 0.8989 (m) REVERT: B 241 GLU cc_start: 0.7597 (tp30) cc_final: 0.7211 (tm-30) REVERT: B 270 ASN cc_start: 0.8142 (t0) cc_final: 0.7353 (t0) REVERT: D 43 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7749 (t0) REVERT: D 80 GLU cc_start: 0.7553 (pm20) cc_final: 0.7246 (pm20) REVERT: D 220 MET cc_start: 0.6196 (mmp) cc_final: 0.5625 (mmt) REVERT: D 327 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7752 (pm20) REVERT: F 103 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8673 (tp) REVERT: F 117 ASP cc_start: 0.8044 (t0) cc_final: 0.7786 (t0) REVERT: F 143 ARG cc_start: 0.7123 (mtp180) cc_final: 0.6669 (ttt-90) REVERT: F 196 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.7997 (p0) REVERT: F 219 ILE cc_start: 0.8916 (mp) cc_final: 0.8712 (tt) REVERT: F 334 SER cc_start: 0.8331 (m) cc_final: 0.7939 (t) REVERT: H 21 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.7175 (m-80) REVERT: H 61 THR cc_start: 0.2817 (OUTLIER) cc_final: 0.1707 (m) REVERT: H 248 ARG cc_start: 0.7621 (mtp180) cc_final: 0.6622 (ttt90) REVERT: H 255 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.5802 (mp10) REVERT: J 46 TYR cc_start: 0.9035 (p90) cc_final: 0.8616 (p90) REVERT: J 352 ILE cc_start: 0.8017 (tt) cc_final: 0.7692 (mm) REVERT: J 373 LYS cc_start: 0.7288 (mmtt) cc_final: 0.7041 (mttp) REVERT: L 69 TYR cc_start: 0.6966 (m-10) cc_final: 0.6200 (m-10) REVERT: L 80 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5558 (tt0) REVERT: N 75 ASP cc_start: 0.8330 (t0) cc_final: 0.7739 (t0) REVERT: P 35 GLU cc_start: 0.7088 (tt0) cc_final: 0.6842 (tt0) outliers start: 116 outliers final: 87 residues processed: 617 average time/residue: 0.6925 time to fit residues: 679.4871 Evaluate side-chains 627 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 529 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 72 TYR Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 386 HIS Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 204 CYS Chi-restraints excluded: chain H residue 255 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 110 PHE Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 228 ASN Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 MET Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 318 THR Chi-restraints excluded: chain L residue 345 GLU Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 185 TYR Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 225 SER Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 300 THR Chi-restraints excluded: chain P residue 345 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 117 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 86 optimal weight: 0.0470 chunk 350 optimal weight: 0.9980 chunk 290 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 HIS ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 HIS H 24 HIS ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 149 HIS ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29244 Z= 0.222 Angle : 0.553 7.659 39858 Z= 0.288 Chirality : 0.045 0.387 4530 Planarity : 0.004 0.064 5093 Dihedral : 4.952 67.882 4184 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.45 % Allowed : 21.65 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3659 helix: 2.39 (0.26), residues: 413 sheet: -1.21 (0.15), residues: 1224 loop : -1.18 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 243 HIS 0.009 0.001 HIS P 149 PHE 0.026 0.001 PHE F 95 TYR 0.017 0.001 TYR H 21 ARG 0.005 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 545 time to evaluate : 3.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 138 CYS cc_start: 0.6480 (OUTLIER) cc_final: 0.6245 (p) REVERT: B 103 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7718 (tp) REVERT: B 131 VAL cc_start: 0.9232 (t) cc_final: 0.9011 (m) REVERT: B 241 GLU cc_start: 0.7607 (tp30) cc_final: 0.7188 (tp30) REVERT: B 270 ASN cc_start: 0.8170 (t0) cc_final: 0.7362 (t0) REVERT: B 366 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8606 (mm) REVERT: D 43 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7992 (t0) REVERT: D 66 LYS cc_start: 0.7210 (tppt) cc_final: 0.6994 (tppp) REVERT: D 80 GLU cc_start: 0.7468 (pm20) cc_final: 0.7144 (pm20) REVERT: D 220 MET cc_start: 0.6179 (mmp) cc_final: 0.5606 (mmt) REVERT: D 327 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: D 345 GLU cc_start: 0.7403 (pm20) cc_final: 0.7117 (pm20) REVERT: F 103 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8651 (tp) REVERT: F 117 ASP cc_start: 0.8077 (t0) cc_final: 0.7815 (t0) REVERT: F 143 ARG cc_start: 0.7133 (mtp180) cc_final: 0.6672 (ttt-90) REVERT: F 196 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8002 (p0) REVERT: F 334 SER cc_start: 0.8355 (m) cc_final: 0.7985 (t) REVERT: H 21 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.7143 (m-80) REVERT: H 234 ARG cc_start: 0.7171 (ptt90) cc_final: 0.6778 (ptt90) REVERT: H 248 ARG cc_start: 0.7685 (mtp180) cc_final: 0.6608 (ttt90) REVERT: H 255 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.5871 (mp10) REVERT: J 45 GLU cc_start: 0.8267 (tp30) cc_final: 0.7861 (tp30) REVERT: J 352 ILE cc_start: 0.8099 (tt) cc_final: 0.7784 (mm) REVERT: J 373 LYS cc_start: 0.7370 (mmtt) cc_final: 0.7104 (mttp) REVERT: L 80 GLU cc_start: 0.5965 (OUTLIER) cc_final: 0.5660 (tt0) REVERT: L 115 THR cc_start: 0.8460 (t) cc_final: 0.8181 (p) REVERT: L 128 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8439 (p) REVERT: N 75 ASP cc_start: 0.8342 (t0) cc_final: 0.7732 (t0) REVERT: N 93 GLN cc_start: 0.7589 (tm-30) cc_final: 0.7228 (tm-30) outliers start: 139 outliers final: 113 residues processed: 642 average time/residue: 0.7000 time to fit residues: 715.6133 Evaluate side-chains 652 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 528 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 386 HIS Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 54 PHE Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain H residue 255 GLN Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 110 PHE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 228 ASN Chi-restraints excluded: chain J residue 238 SER Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 70 MET Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain L residue 263 ARG Chi-restraints excluded: chain L residue 318 THR Chi-restraints excluded: chain L residue 345 GLU Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 185 TYR Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 225 SER Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 149 HIS Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 265 THR Chi-restraints excluded: chain P residue 300 THR Chi-restraints excluded: chain P residue 345 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 337 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 199 optimal weight: 0.8980 chunk 255 optimal weight: 0.7980 chunk 198 optimal weight: 0.9990 chunk 294 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 348 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 212 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN D 53 GLN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 HIS ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 HIS ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 335 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29244 Z= 0.190 Angle : 0.550 6.447 39858 Z= 0.287 Chirality : 0.045 0.385 4530 Planarity : 0.004 0.061 5093 Dihedral : 4.918 68.482 4184 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.07 % Allowed : 22.22 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3659 helix: 2.47 (0.26), residues: 413 sheet: -1.16 (0.15), residues: 1224 loop : -1.13 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 243 HIS 0.008 0.001 HIS P 149 PHE 0.011 0.001 PHE H 54 TYR 0.017 0.001 TYR L 21 ARG 0.005 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 541 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 138 CYS cc_start: 0.6416 (OUTLIER) cc_final: 0.6196 (p) REVERT: B 103 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7671 (tp) REVERT: B 366 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8633 (mm) REVERT: D 43 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7938 (t0) REVERT: D 80 GLU cc_start: 0.7457 (pm20) cc_final: 0.7116 (pm20) REVERT: D 220 MET cc_start: 0.6151 (mmp) cc_final: 0.5582 (mmt) REVERT: D 327 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: F 95 PHE cc_start: 0.6576 (p90) cc_final: 0.6323 (p90) REVERT: F 103 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8651 (tp) REVERT: F 117 ASP cc_start: 0.8088 (t0) cc_final: 0.7818 (t0) REVERT: F 143 ARG cc_start: 0.7129 (mtp180) cc_final: 0.6669 (ttt-90) REVERT: F 196 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7977 (p0) REVERT: F 334 SER cc_start: 0.8355 (m) cc_final: 0.7994 (t) REVERT: H 21 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: H 61 THR cc_start: 0.2972 (OUTLIER) cc_final: 0.1881 (m) REVERT: H 248 ARG cc_start: 0.7537 (mtp180) cc_final: 0.6379 (ttt90) REVERT: J 352 ILE cc_start: 0.8095 (tt) cc_final: 0.7781 (mm) REVERT: J 373 LYS cc_start: 0.7508 (mmtt) cc_final: 0.7243 (mttp) REVERT: L 69 TYR cc_start: 0.7028 (m-10) cc_final: 0.6302 (m-10) REVERT: L 80 GLU cc_start: 0.5958 (OUTLIER) cc_final: 0.5603 (tt0) REVERT: L 115 THR cc_start: 0.8450 (t) cc_final: 0.8236 (p) REVERT: L 248 ARG cc_start: 0.7977 (mtt-85) cc_final: 0.7426 (ttm-80) REVERT: N 75 ASP cc_start: 0.8323 (t0) cc_final: 0.7756 (t0) outliers start: 127 outliers final: 102 residues processed: 627 average time/residue: 0.7188 time to fit residues: 712.6759 Evaluate side-chains 647 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 535 time to evaluate : 4.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 386 HIS Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 110 PHE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 269 THR Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 70 MET Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 263 ARG Chi-restraints excluded: chain L residue 318 THR Chi-restraints excluded: chain L residue 345 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 185 TYR Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 225 SER Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 328 CYS Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain N residue 428 LEU Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 263 ARG Chi-restraints excluded: chain P residue 300 THR Chi-restraints excluded: chain P residue 345 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 215 optimal weight: 0.5980 chunk 139 optimal weight: 9.9990 chunk 208 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 274 optimal weight: 20.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 HIS ** F 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 HIS H 255 GLN ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29244 Z= 0.254 Angle : 0.567 6.459 39858 Z= 0.297 Chirality : 0.045 0.389 4530 Planarity : 0.004 0.068 5093 Dihedral : 5.000 68.787 4184 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.51 % Allowed : 21.87 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3659 helix: 2.48 (0.26), residues: 413 sheet: -1.25 (0.15), residues: 1228 loop : -1.20 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 282 HIS 0.007 0.001 HIS B 331 PHE 0.018 0.001 PHE H 54 TYR 0.029 0.001 TYR N 107 ARG 0.005 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 536 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 CYS cc_start: 0.6505 (OUTLIER) cc_final: 0.6275 (p) REVERT: B 103 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7743 (tp) REVERT: B 366 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8674 (mm) REVERT: D 21 TYR cc_start: 0.7239 (OUTLIER) cc_final: 0.6812 (m-80) REVERT: D 43 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8021 (t0) REVERT: D 80 GLU cc_start: 0.7511 (pm20) cc_final: 0.7179 (pm20) REVERT: D 220 MET cc_start: 0.6249 (mmp) cc_final: 0.5689 (mmt) REVERT: D 327 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: F 39 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7868 (p) REVERT: F 95 PHE cc_start: 0.6970 (p90) cc_final: 0.6758 (p90) REVERT: F 103 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8684 (tp) REVERT: F 117 ASP cc_start: 0.8182 (t0) cc_final: 0.7841 (t0) REVERT: F 143 ARG cc_start: 0.7149 (mtp180) cc_final: 0.6672 (ttt-90) REVERT: F 196 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8095 (p0) REVERT: F 334 SER cc_start: 0.8402 (m) cc_final: 0.8029 (t) REVERT: H 21 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.6997 (m-80) REVERT: H 61 THR cc_start: 0.3113 (OUTLIER) cc_final: 0.2297 (m) REVERT: H 234 ARG cc_start: 0.7155 (ptt90) cc_final: 0.6758 (ptt90) REVERT: H 248 ARG cc_start: 0.7678 (mtp180) cc_final: 0.6514 (ttt90) REVERT: J 218 ASP cc_start: 0.7793 (t0) cc_final: 0.7579 (t0) REVERT: J 352 ILE cc_start: 0.8212 (tt) cc_final: 0.7908 (mm) REVERT: L 80 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5749 (tt0) REVERT: L 115 THR cc_start: 0.8470 (t) cc_final: 0.8206 (p) REVERT: N 75 ASP cc_start: 0.8385 (t0) cc_final: 0.7747 (t0) REVERT: N 93 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7266 (tm-30) outliers start: 141 outliers final: 117 residues processed: 634 average time/residue: 0.7609 time to fit residues: 765.4963 Evaluate side-chains 654 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 525 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 386 HIS Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 54 PHE Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 110 PHE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 228 ASN Chi-restraints excluded: chain J residue 238 SER Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 269 THR Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 MET Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 204 CYS Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain L residue 263 ARG Chi-restraints excluded: chain L residue 318 THR Chi-restraints excluded: chain L residue 345 GLU Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 185 TYR Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 225 SER Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 346 VAL Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 367 VAL Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain N residue 428 LEU Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 149 HIS Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 263 ARG Chi-restraints excluded: chain P residue 265 THR Chi-restraints excluded: chain P residue 300 THR Chi-restraints excluded: chain P residue 345 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 317 optimal weight: 0.5980 chunk 334 optimal weight: 0.9980 chunk 304 optimal weight: 0.9980 chunk 325 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 255 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 293 optimal weight: 0.9980 chunk 307 optimal weight: 4.9990 chunk 324 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 364 ASN ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29244 Z= 0.191 Angle : 0.558 11.968 39858 Z= 0.288 Chirality : 0.045 0.386 4530 Planarity : 0.004 0.069 5093 Dihedral : 4.940 69.458 4184 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.42 % Allowed : 21.93 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3659 helix: 2.51 (0.26), residues: 413 sheet: -1.20 (0.15), residues: 1228 loop : -1.14 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 243 HIS 0.009 0.001 HIS J 333 PHE 0.011 0.001 PHE P 54 TYR 0.027 0.001 TYR L 21 ARG 0.005 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 546 time to evaluate : 3.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 CYS cc_start: 0.6438 (OUTLIER) cc_final: 0.6208 (p) REVERT: B 103 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7666 (tp) REVERT: B 328 CYS cc_start: 0.6066 (m) cc_final: 0.5711 (m) REVERT: B 366 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8591 (mm) REVERT: D 21 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6966 (m-80) REVERT: D 43 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8043 (t0) REVERT: D 141 GLU cc_start: 0.8083 (pm20) cc_final: 0.6959 (pt0) REVERT: D 220 MET cc_start: 0.6220 (mmp) cc_final: 0.5668 (mmt) REVERT: D 327 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7740 (pm20) REVERT: F 95 PHE cc_start: 0.6891 (p90) cc_final: 0.6691 (p90) REVERT: F 103 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8687 (tp) REVERT: F 117 ASP cc_start: 0.8109 (t0) cc_final: 0.7820 (t0) REVERT: F 143 ARG cc_start: 0.7138 (mtp180) cc_final: 0.6644 (ttt-90) REVERT: F 196 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.8109 (p0) REVERT: F 334 SER cc_start: 0.8397 (m) cc_final: 0.8030 (t) REVERT: H 21 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.7178 (m-80) REVERT: H 61 THR cc_start: 0.2654 (OUTLIER) cc_final: 0.1915 (m) REVERT: H 234 ARG cc_start: 0.7140 (ptt90) cc_final: 0.6775 (ptt90) REVERT: J 218 ASP cc_start: 0.7780 (t0) cc_final: 0.7560 (t0) REVERT: J 352 ILE cc_start: 0.8249 (tt) cc_final: 0.7991 (mm) REVERT: L 80 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5762 (tt0) REVERT: L 232 TYR cc_start: 0.6304 (m-10) cc_final: 0.5988 (m-10) REVERT: L 248 ARG cc_start: 0.7977 (mtt-85) cc_final: 0.7418 (ttm-80) REVERT: N 75 ASP cc_start: 0.8318 (t0) cc_final: 0.7741 (t0) REVERT: N 218 ASP cc_start: 0.7723 (t0) cc_final: 0.7513 (t0) outliers start: 138 outliers final: 118 residues processed: 640 average time/residue: 0.7386 time to fit residues: 752.5874 Evaluate side-chains 662 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 533 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 386 HIS Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 54 PHE Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 110 PHE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 238 SER Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 269 THR Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 MET Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 204 CYS Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain L residue 263 ARG Chi-restraints excluded: chain L residue 318 THR Chi-restraints excluded: chain L residue 345 GLU Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 185 TYR Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 225 SER Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 364 ASN Chi-restraints excluded: chain N residue 367 VAL Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain N residue 428 LEU Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 202 TYR Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 263 ARG Chi-restraints excluded: chain P residue 300 THR Chi-restraints excluded: chain P residue 345 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 213 optimal weight: 1.9990 chunk 343 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 163 optimal weight: 0.0270 chunk 239 optimal weight: 2.9990 chunk 360 optimal weight: 1.9990 chunk 331 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 HIS ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 364 ASN ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.359 29244 Z= 0.324 Angle : 0.681 59.199 39858 Z= 0.378 Chirality : 0.045 0.386 4530 Planarity : 0.004 0.069 5093 Dihedral : 4.939 69.468 4184 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.23 % Allowed : 22.51 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3659 helix: 2.51 (0.26), residues: 413 sheet: -1.21 (0.15), residues: 1228 loop : -1.14 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 243 HIS 0.014 0.001 HIS P 99 PHE 0.029 0.001 PHE H 145 TYR 0.025 0.001 TYR L 21 ARG 0.005 0.000 ARG P 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7318 Ramachandran restraints generated. 3659 Oldfield, 0 Emsley, 3659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 536 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 CYS cc_start: 0.6444 (OUTLIER) cc_final: 0.6208 (p) REVERT: B 103 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7682 (tp) REVERT: B 366 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8629 (mm) REVERT: B 370 CYS cc_start: 0.7212 (t) cc_final: 0.6886 (t) REVERT: D 21 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: D 43 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8042 (t0) REVERT: D 80 GLU cc_start: 0.7488 (pm20) cc_final: 0.7167 (pm20) REVERT: D 141 GLU cc_start: 0.8085 (pm20) cc_final: 0.7121 (pt0) REVERT: D 220 MET cc_start: 0.6231 (mmp) cc_final: 0.5673 (mmt) REVERT: D 327 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: F 103 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8694 (tp) REVERT: F 117 ASP cc_start: 0.8114 (t0) cc_final: 0.7827 (t0) REVERT: F 143 ARG cc_start: 0.7124 (mtp180) cc_final: 0.6646 (ttt-90) REVERT: F 196 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8114 (p0) REVERT: F 334 SER cc_start: 0.8400 (m) cc_final: 0.8032 (t) REVERT: H 21 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: H 61 THR cc_start: 0.2629 (OUTLIER) cc_final: 0.1943 (m) REVERT: H 234 ARG cc_start: 0.7152 (ptt90) cc_final: 0.6777 (ptt90) REVERT: J 218 ASP cc_start: 0.7782 (t0) cc_final: 0.7563 (t0) REVERT: J 352 ILE cc_start: 0.8220 (tt) cc_final: 0.7957 (mm) REVERT: L 80 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5756 (tt0) REVERT: L 232 TYR cc_start: 0.6290 (m-10) cc_final: 0.5978 (m-10) REVERT: L 248 ARG cc_start: 0.7991 (mtt-85) cc_final: 0.7422 (ttm-80) REVERT: N 75 ASP cc_start: 0.8321 (t0) cc_final: 0.7742 (t0) REVERT: N 218 ASP cc_start: 0.7724 (t0) cc_final: 0.7518 (t0) outliers start: 132 outliers final: 118 residues processed: 626 average time/residue: 0.7617 time to fit residues: 755.4428 Evaluate side-chains 667 residues out of total 3123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 538 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 196 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain F residue 386 HIS Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 54 PHE Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 202 TYR Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 221 ASN Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 102 GLN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 110 PHE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 238 SER Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 261 ILE Chi-restraints excluded: chain J residue 269 THR Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 366 ILE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 MET Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 204 CYS Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain L residue 263 ARG Chi-restraints excluded: chain L residue 318 THR Chi-restraints excluded: chain L residue 345 GLU Chi-restraints excluded: chain L residue 411 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 100 ASN Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 185 TYR Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 214 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 225 SER Chi-restraints excluded: chain N residue 238 SER Chi-restraints excluded: chain N residue 332 SER Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 364 ASN Chi-restraints excluded: chain N residue 367 VAL Chi-restraints excluded: chain N residue 386 HIS Chi-restraints excluded: chain N residue 428 LEU Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 108 CYS Chi-restraints excluded: chain P residue 227 LYS Chi-restraints excluded: chain P residue 263 ARG Chi-restraints excluded: chain P residue 300 THR Chi-restraints excluded: chain P residue 345 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 228 optimal weight: 0.0770 chunk 305 optimal weight: 0.4980 chunk 87 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 287 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 295 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 364 ASN ** N 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.197920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.160758 restraints weight = 99817.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.163092 restraints weight = 90637.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.165253 restraints weight = 59392.925| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.359 29244 Z= 0.320 Angle : 0.648 47.200 39858 Z= 0.354 Chirality : 0.045 0.386 4530 Planarity : 0.004 0.069 5093 Dihedral : 4.939 69.468 4184 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.13 % Allowed : 22.57 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3659 helix: 2.51 (0.26), residues: 413 sheet: -1.21 (0.15), residues: 1228 loop : -1.14 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 243 HIS 0.014 0.001 HIS P 99 PHE 0.029 0.001 PHE H 145 TYR 0.025 0.001 TYR L 21 ARG 0.005 0.000 ARG P 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11730.97 seconds wall clock time: 203 minutes 4.14 seconds (12184.14 seconds total)