Starting phenix.real_space_refine on Sun Feb 18 13:42:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf4_32460/02_2024/7wf4_32460_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf4_32460/02_2024/7wf4_32460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf4_32460/02_2024/7wf4_32460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf4_32460/02_2024/7wf4_32460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf4_32460/02_2024/7wf4_32460_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf4_32460/02_2024/7wf4_32460_neut_updated.pdb" } resolution = 3.4 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= 0.015 sd= 1.348 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 12 5.49 5 S 120 5.16 5 C 14196 2.51 5 N 3736 2.21 5 O 4076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 234": "NH1" <-> "NH2" Residue "D PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D ARG 373": "NH1" <-> "NH2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 423": "OD1" <-> "OD2" Residue "D ASP 449": "OD1" <-> "OD2" Residue "D PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 489": "NH1" <-> "NH2" Residue "G ASP 85": "OD1" <-> "OD2" Residue "G PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 222": "NH1" <-> "NH2" Residue "G TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 298": "NH1" <-> "NH2" Residue "I ASP 85": "OD1" <-> "OD2" Residue "I PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 222": "NH1" <-> "NH2" Residue "I TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 298": "NH1" <-> "NH2" Residue "J PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 146": "OE1" <-> "OE2" Residue "J ASP 150": "OD1" <-> "OD2" Residue "J GLU 183": "OE1" <-> "OE2" Residue "J ARG 198": "NH1" <-> "NH2" Residue "J PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 85": "OD1" <-> "OD2" Residue "M PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 222": "NH1" <-> "NH2" Residue "M TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 298": "NH1" <-> "NH2" Residue "N PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 146": "OE1" <-> "OE2" Residue "N ASP 150": "OD1" <-> "OD2" Residue "N GLU 183": "OE1" <-> "OE2" Residue "N ARG 198": "NH1" <-> "NH2" Residue "N PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 146": "OE1" <-> "OE2" Residue "O ASP 150": "OD1" <-> "OD2" Residue "O GLU 183": "OE1" <-> "OE2" Residue "O ARG 198": "NH1" <-> "NH2" Residue "O PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 146": "OE1" <-> "OE2" Residue "P ASP 150": "OD1" <-> "OD2" Residue "P GLU 183": "OE1" <-> "OE2" Residue "P ARG 198": "NH1" <-> "NH2" Residue "P PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 85": "OD1" <-> "OD2" Residue "o PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 222": "NH1" <-> "NH2" Residue "o TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 298": "NH1" <-> "NH2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 423": "OD1" <-> "OD2" Residue "B ASP 449": "OD1" <-> "OD2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "F TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 234": "NH1" <-> "NH2" Residue "F PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "F PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 325": "NH1" <-> "NH2" Residue "F ARG 350": "NH1" <-> "NH2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "F ARG 396": "NH1" <-> "NH2" Residue "F PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 423": "OD1" <-> "OD2" Residue "F ASP 449": "OD1" <-> "OD2" Residue "F PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 489": "NH1" <-> "NH2" Residue "H TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 234": "NH1" <-> "NH2" Residue "H PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 313": "NH1" <-> "NH2" Residue "H PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 325": "NH1" <-> "NH2" Residue "H ARG 350": "NH1" <-> "NH2" Residue "H ARG 373": "NH1" <-> "NH2" Residue "H ARG 396": "NH1" <-> "NH2" Residue "H PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 423": "OD1" <-> "OD2" Residue "H ASP 449": "OD1" <-> "OD2" Residue "H PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 489": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22143 Number of models: 1 Model: "" Number of chains: 25 Chain: "D" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2017 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 242} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "O" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "o" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2017 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 242} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2017 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 242} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2017 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 242} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "I" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "M" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "o" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 11.01, per 1000 atoms: 0.50 Number of scatterers: 22143 At special positions: 0 Unit cell: (130.416, 131.274, 163.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 120 16.00 P 12 15.00 O 4076 8.00 N 3736 7.00 C 14196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS J 101 " - pdb=" SG CYS J 123 " distance=2.03 Simple disulfide: pdb=" SG CYS N 101 " - pdb=" SG CYS N 123 " distance=2.03 Simple disulfide: pdb=" SG CYS O 101 " - pdb=" SG CYS O 123 " distance=2.04 Simple disulfide: pdb=" SG CYS P 101 " - pdb=" SG CYS P 123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.63 Conformation dependent library (CDL) restraints added in 4.2 seconds 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 16 sheets defined 54.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 231 through 253 Processing helix chain 'D' and resid 294 through 315 removed outlier: 3.998A pdb=" N VAL D 298 " --> pdb=" O PRO D 294 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 325 Processing helix chain 'D' and resid 328 through 352 Proline residue: D 338 - end of helix removed outlier: 3.630A pdb=" N ALA D 348 " --> pdb=" O GLY D 344 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 379 removed outlier: 3.726A pdb=" N LEU D 368 " --> pdb=" O ARG D 364 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 369 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL D 371 " --> pdb=" O ARG D 367 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG D 373 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N PHE D 375 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS D 376 " --> pdb=" O PHE D 372 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU D 377 " --> pdb=" O ARG D 373 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG D 379 " --> pdb=" O PHE D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 393 Processing helix chain 'D' and resid 395 through 420 removed outlier: 3.694A pdb=" N GLU D 420 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 442 removed outlier: 3.714A pdb=" N PHE D 435 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TRP D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TRP D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 472 removed outlier: 3.564A pdb=" N VAL D 460 " --> pdb=" O GLY D 456 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 488 Processing helix chain 'G' and resid 66 through 79 removed outlier: 3.727A pdb=" N ASN G 79 " --> pdb=" O LEU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 106 removed outlier: 6.175A pdb=" N ALA G 95 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS G 104 " --> pdb=" O ASN G 101 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS G 106 " --> pdb=" O ILE G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 126 through 128 No H-bonds generated for 'chain 'G' and resid 126 through 128' Processing helix chain 'G' and resid 133 through 146 Processing helix chain 'G' and resid 166 through 178 Processing helix chain 'G' and resid 192 through 204 Processing helix chain 'G' and resid 223 through 227 Processing helix chain 'G' and resid 229 through 235 Processing helix chain 'G' and resid 247 through 249 No H-bonds generated for 'chain 'G' and resid 247 through 249' Processing helix chain 'G' and resid 271 through 277 Processing helix chain 'G' and resid 281 through 299 Processing helix chain 'G' and resid 303 through 310 Processing helix chain 'G' and resid 327 through 340 removed outlier: 3.846A pdb=" N GLY G 335 " --> pdb=" O MET G 331 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA G 336 " --> pdb=" O GLU G 332 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE G 337 " --> pdb=" O ASN G 333 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLN G 338 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL G 339 " --> pdb=" O GLY G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 355 Processing helix chain 'I' and resid 66 through 79 removed outlier: 3.728A pdb=" N ASN I 79 " --> pdb=" O LEU I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 106 removed outlier: 6.175A pdb=" N ALA I 95 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS I 104 " --> pdb=" O ASN I 101 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS I 106 " --> pdb=" O ILE I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 112 No H-bonds generated for 'chain 'I' and resid 110 through 112' Processing helix chain 'I' and resid 126 through 128 No H-bonds generated for 'chain 'I' and resid 126 through 128' Processing helix chain 'I' and resid 133 through 146 Processing helix chain 'I' and resid 166 through 178 Processing helix chain 'I' and resid 192 through 204 Processing helix chain 'I' and resid 223 through 227 Processing helix chain 'I' and resid 229 through 235 Processing helix chain 'I' and resid 247 through 249 No H-bonds generated for 'chain 'I' and resid 247 through 249' Processing helix chain 'I' and resid 271 through 277 Processing helix chain 'I' and resid 281 through 299 Processing helix chain 'I' and resid 303 through 310 Processing helix chain 'I' and resid 327 through 340 removed outlier: 3.847A pdb=" N GLY I 335 " --> pdb=" O MET I 331 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA I 336 " --> pdb=" O GLU I 332 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE I 337 " --> pdb=" O ASN I 333 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLN I 338 " --> pdb=" O ILE I 334 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL I 339 " --> pdb=" O GLY I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 355 Processing helix chain 'J' and resid 119 through 124 removed outlier: 3.916A pdb=" N GLN J 124 " --> pdb=" O LYS J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 139 No H-bonds generated for 'chain 'J' and resid 137 through 139' Processing helix chain 'J' and resid 156 through 165 removed outlier: 3.541A pdb=" N TYR J 163 " --> pdb=" O ILE J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 187 Processing helix chain 'J' and resid 191 through 200 Processing helix chain 'M' and resid 66 through 79 removed outlier: 3.728A pdb=" N ASN M 79 " --> pdb=" O LEU M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 106 removed outlier: 6.174A pdb=" N ALA M 95 " --> pdb=" O ALA M 92 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS M 104 " --> pdb=" O ASN M 101 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS M 106 " --> pdb=" O ILE M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 112 No H-bonds generated for 'chain 'M' and resid 110 through 112' Processing helix chain 'M' and resid 126 through 128 No H-bonds generated for 'chain 'M' and resid 126 through 128' Processing helix chain 'M' and resid 133 through 146 Processing helix chain 'M' and resid 166 through 178 Processing helix chain 'M' and resid 192 through 204 Processing helix chain 'M' and resid 223 through 227 Processing helix chain 'M' and resid 229 through 235 Processing helix chain 'M' and resid 247 through 249 No H-bonds generated for 'chain 'M' and resid 247 through 249' Processing helix chain 'M' and resid 271 through 277 Processing helix chain 'M' and resid 281 through 299 Processing helix chain 'M' and resid 303 through 310 Processing helix chain 'M' and resid 327 through 340 removed outlier: 3.847A pdb=" N GLY M 335 " --> pdb=" O MET M 331 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA M 336 " --> pdb=" O GLU M 332 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE M 337 " --> pdb=" O ASN M 333 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLN M 338 " --> pdb=" O ILE M 334 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL M 339 " --> pdb=" O GLY M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 355 Processing helix chain 'N' and resid 119 through 124 removed outlier: 3.916A pdb=" N GLN N 124 " --> pdb=" O LYS N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 139 No H-bonds generated for 'chain 'N' and resid 137 through 139' Processing helix chain 'N' and resid 156 through 165 removed outlier: 3.540A pdb=" N TYR N 163 " --> pdb=" O ILE N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 187 Processing helix chain 'N' and resid 191 through 200 Processing helix chain 'O' and resid 119 through 124 removed outlier: 3.915A pdb=" N GLN O 124 " --> pdb=" O LYS O 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 139 No H-bonds generated for 'chain 'O' and resid 137 through 139' Processing helix chain 'O' and resid 156 through 165 removed outlier: 3.540A pdb=" N TYR O 163 " --> pdb=" O ILE O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 177 through 187 Processing helix chain 'O' and resid 191 through 200 Processing helix chain 'P' and resid 119 through 124 removed outlier: 3.915A pdb=" N GLN P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 139 No H-bonds generated for 'chain 'P' and resid 137 through 139' Processing helix chain 'P' and resid 156 through 165 removed outlier: 3.541A pdb=" N TYR P 163 " --> pdb=" O ILE P 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 187 Processing helix chain 'P' and resid 191 through 200 Processing helix chain 'o' and resid 66 through 79 removed outlier: 3.728A pdb=" N ASN o 79 " --> pdb=" O LEU o 75 " (cutoff:3.500A) Processing helix chain 'o' and resid 90 through 106 removed outlier: 6.175A pdb=" N ALA o 95 " --> pdb=" O ALA o 92 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS o 104 " --> pdb=" O ASN o 101 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS o 106 " --> pdb=" O ILE o 103 " (cutoff:3.500A) Processing helix chain 'o' and resid 110 through 112 No H-bonds generated for 'chain 'o' and resid 110 through 112' Processing helix chain 'o' and resid 126 through 128 No H-bonds generated for 'chain 'o' and resid 126 through 128' Processing helix chain 'o' and resid 133 through 146 Processing helix chain 'o' and resid 166 through 178 Processing helix chain 'o' and resid 192 through 204 Processing helix chain 'o' and resid 223 through 227 Processing helix chain 'o' and resid 229 through 235 Processing helix chain 'o' and resid 247 through 249 No H-bonds generated for 'chain 'o' and resid 247 through 249' Processing helix chain 'o' and resid 271 through 277 Processing helix chain 'o' and resid 281 through 299 Processing helix chain 'o' and resid 303 through 310 Processing helix chain 'o' and resid 327 through 340 removed outlier: 3.847A pdb=" N GLY o 335 " --> pdb=" O MET o 331 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA o 336 " --> pdb=" O GLU o 332 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE o 337 " --> pdb=" O ASN o 333 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLN o 338 " --> pdb=" O ILE o 334 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL o 339 " --> pdb=" O GLY o 335 " (cutoff:3.500A) Processing helix chain 'o' and resid 345 through 355 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 231 through 253 Processing helix chain 'B' and resid 294 through 315 removed outlier: 3.997A pdb=" N VAL B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 328 through 352 Proline residue: B 338 - end of helix removed outlier: 3.630A pdb=" N ALA B 348 " --> pdb=" O GLY B 344 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 379 removed outlier: 3.727A pdb=" N LEU B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N PHE B 375 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG B 379 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 395 through 420 removed outlier: 3.693A pdb=" N GLU B 420 " --> pdb=" O VAL B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 442 removed outlier: 3.714A pdb=" N PHE B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TRP B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 472 removed outlier: 3.564A pdb=" N VAL B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 231 through 253 Processing helix chain 'F' and resid 294 through 315 removed outlier: 3.997A pdb=" N VAL F 298 " --> pdb=" O PRO F 294 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU F 299 " --> pdb=" O PHE F 295 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR F 300 " --> pdb=" O PHE F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 325 Processing helix chain 'F' and resid 328 through 352 Proline residue: F 338 - end of helix removed outlier: 3.630A pdb=" N ALA F 348 " --> pdb=" O GLY F 344 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN F 351 " --> pdb=" O LEU F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 379 removed outlier: 3.726A pdb=" N LEU F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 369 " --> pdb=" O VAL F 365 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL F 371 " --> pdb=" O ARG F 367 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG F 373 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N PHE F 375 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS F 376 " --> pdb=" O PHE F 372 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N SER F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG F 379 " --> pdb=" O PHE F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 393 Processing helix chain 'F' and resid 395 through 420 removed outlier: 3.694A pdb=" N GLU F 420 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 442 removed outlier: 3.715A pdb=" N PHE F 435 " --> pdb=" O ILE F 431 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP F 436 " --> pdb=" O PRO F 432 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TRP F 437 " --> pdb=" O ASP F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 472 removed outlier: 3.564A pdb=" N VAL F 460 " --> pdb=" O GLY F 456 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL F 469 " --> pdb=" O ALA F 465 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU F 470 " --> pdb=" O ILE F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 488 Processing helix chain 'H' and resid 217 through 225 Processing helix chain 'H' and resid 231 through 253 Processing helix chain 'H' and resid 294 through 315 removed outlier: 3.997A pdb=" N VAL H 298 " --> pdb=" O PRO H 294 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU H 299 " --> pdb=" O PHE H 295 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR H 300 " --> pdb=" O PHE H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 325 Processing helix chain 'H' and resid 328 through 352 Proline residue: H 338 - end of helix removed outlier: 3.629A pdb=" N ALA H 348 " --> pdb=" O GLY H 344 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN H 351 " --> pdb=" O LEU H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 379 removed outlier: 3.725A pdb=" N LEU H 368 " --> pdb=" O ARG H 364 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 369 " --> pdb=" O VAL H 365 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL H 371 " --> pdb=" O ARG H 367 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE H 372 " --> pdb=" O LEU H 368 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG H 373 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE H 374 " --> pdb=" O ARG H 370 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N PHE H 375 " --> pdb=" O VAL H 371 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS H 376 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU H 377 " --> pdb=" O ARG H 373 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER H 378 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG H 379 " --> pdb=" O PHE H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 393 Processing helix chain 'H' and resid 395 through 420 removed outlier: 3.693A pdb=" N GLU H 420 " --> pdb=" O VAL H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 442 removed outlier: 3.714A pdb=" N PHE H 435 " --> pdb=" O ILE H 431 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP H 436 " --> pdb=" O PRO H 432 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TRP H 437 " --> pdb=" O ASP H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 472 removed outlier: 3.565A pdb=" N VAL H 460 " --> pdb=" O GLY H 456 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU H 463 " --> pdb=" O ILE H 459 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL H 469 " --> pdb=" O ALA H 465 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU H 470 " --> pdb=" O ILE H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 488 Processing sheet with id= A, first strand: chain 'G' and resid 39 through 41 Processing sheet with id= B, first strand: chain 'G' and resid 52 through 54 removed outlier: 7.983A pdb=" N GLY G 53 " --> pdb=" O SER G 318 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL G 320 " --> pdb=" O GLY G 53 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA G 240 " --> pdb=" O SER G 318 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL G 320 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR G 242 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU G 322 " --> pdb=" O THR G 242 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA G 215 " --> pdb=" O MET G 241 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 83 through 85 removed outlier: 6.380A pdb=" N VAL G 114 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL G 154 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ILE G 119 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE G 156 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR G 184 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ALA G 157 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLY G 186 " --> pdb=" O ALA G 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'I' and resid 39 through 41 Processing sheet with id= E, first strand: chain 'I' and resid 52 through 54 removed outlier: 7.983A pdb=" N GLY I 53 " --> pdb=" O SER I 318 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL I 320 " --> pdb=" O GLY I 53 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA I 240 " --> pdb=" O SER I 318 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL I 320 " --> pdb=" O ALA I 240 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR I 242 " --> pdb=" O VAL I 320 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU I 322 " --> pdb=" O THR I 242 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA I 215 " --> pdb=" O MET I 241 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'I' and resid 83 through 85 removed outlier: 6.378A pdb=" N VAL I 114 " --> pdb=" O PHE I 84 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL I 154 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ILE I 119 " --> pdb=" O VAL I 154 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE I 156 " --> pdb=" O ILE I 119 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR I 184 " --> pdb=" O VAL I 155 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ALA I 157 " --> pdb=" O TYR I 184 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLY I 186 " --> pdb=" O ALA I 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'J' and resid 113 through 118 removed outlier: 6.298A pdb=" N TYR J 147 " --> pdb=" O ASN J 109 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'M' and resid 39 through 41 Processing sheet with id= I, first strand: chain 'M' and resid 52 through 54 removed outlier: 7.983A pdb=" N GLY M 53 " --> pdb=" O SER M 318 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL M 320 " --> pdb=" O GLY M 53 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA M 240 " --> pdb=" O SER M 318 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL M 320 " --> pdb=" O ALA M 240 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR M 242 " --> pdb=" O VAL M 320 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU M 322 " --> pdb=" O THR M 242 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA M 215 " --> pdb=" O MET M 241 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'M' and resid 83 through 85 removed outlier: 6.379A pdb=" N VAL M 114 " --> pdb=" O PHE M 84 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL M 154 " --> pdb=" O THR M 117 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ILE M 119 " --> pdb=" O VAL M 154 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE M 156 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR M 184 " --> pdb=" O VAL M 155 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ALA M 157 " --> pdb=" O TYR M 184 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLY M 186 " --> pdb=" O ALA M 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'N' and resid 113 through 118 removed outlier: 6.299A pdb=" N TYR N 147 " --> pdb=" O ASN N 109 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 113 through 118 removed outlier: 6.299A pdb=" N TYR O 147 " --> pdb=" O ASN O 109 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'P' and resid 113 through 118 removed outlier: 6.298A pdb=" N TYR P 147 " --> pdb=" O ASN P 109 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'o' and resid 39 through 41 Processing sheet with id= O, first strand: chain 'o' and resid 52 through 54 removed outlier: 7.983A pdb=" N GLY o 53 " --> pdb=" O SER o 318 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL o 320 " --> pdb=" O GLY o 53 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA o 240 " --> pdb=" O SER o 318 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL o 320 " --> pdb=" O ALA o 240 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR o 242 " --> pdb=" O VAL o 320 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU o 322 " --> pdb=" O THR o 242 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA o 215 " --> pdb=" O MET o 241 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'o' and resid 83 through 85 removed outlier: 6.380A pdb=" N VAL o 114 " --> pdb=" O PHE o 84 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL o 154 " --> pdb=" O THR o 117 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ILE o 119 " --> pdb=" O VAL o 154 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE o 156 " --> pdb=" O ILE o 119 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR o 184 " --> pdb=" O VAL o 155 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ALA o 157 " --> pdb=" O TYR o 184 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLY o 186 " --> pdb=" O ALA o 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= P 924 hydrogen bonds defined for protein. 2628 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: 6.53 Time building geometry restraints manager: 9.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3536 1.31 - 1.44: 6180 1.44 - 1.57: 12620 1.57 - 1.70: 20 1.70 - 1.83: 192 Bond restraints: 22548 Sorted by residual: bond pdb=" C1B NAP I 401 " pdb=" C2B NAP I 401 " ideal model delta sigma weight residual 1.528 1.309 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C1B NAP G 401 " pdb=" C2B NAP G 401 " ideal model delta sigma weight residual 1.528 1.309 0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C1B NAP o 401 " pdb=" C2B NAP o 401 " ideal model delta sigma weight residual 1.528 1.310 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C1B NAP M 401 " pdb=" C2B NAP M 401 " ideal model delta sigma weight residual 1.528 1.311 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C4D NAP I 401 " pdb=" O4D NAP I 401 " ideal model delta sigma weight residual 1.447 1.304 0.143 2.00e-02 2.50e+03 5.08e+01 ... (remaining 22543 not shown) Histogram of bond angle deviations from ideal: 96.75 - 104.24: 384 104.24 - 111.72: 9787 111.72 - 119.21: 8540 119.21 - 126.70: 11487 126.70 - 134.18: 354 Bond angle restraints: 30552 Sorted by residual: angle pdb=" N GLU B 349 " pdb=" CA GLU B 349 " pdb=" C GLU B 349 " ideal model delta sigma weight residual 111.14 119.64 -8.50 1.08e+00 8.57e-01 6.19e+01 angle pdb=" N GLU F 349 " pdb=" CA GLU F 349 " pdb=" C GLU F 349 " ideal model delta sigma weight residual 111.14 119.59 -8.45 1.08e+00 8.57e-01 6.13e+01 angle pdb=" N GLU D 349 " pdb=" CA GLU D 349 " pdb=" C GLU D 349 " ideal model delta sigma weight residual 111.14 119.59 -8.45 1.08e+00 8.57e-01 6.12e+01 angle pdb=" N GLU H 349 " pdb=" CA GLU H 349 " pdb=" C GLU H 349 " ideal model delta sigma weight residual 111.14 119.56 -8.42 1.08e+00 8.57e-01 6.08e+01 angle pdb=" N MET D 358 " pdb=" CA MET D 358 " pdb=" C MET D 358 " ideal model delta sigma weight residual 110.80 96.75 14.05 2.13e+00 2.20e-01 4.35e+01 ... (remaining 30547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 12187 17.03 - 34.06: 1047 34.06 - 51.09: 260 51.09 - 68.12: 78 68.12 - 85.15: 24 Dihedral angle restraints: 13596 sinusoidal: 5656 harmonic: 7940 Sorted by residual: dihedral pdb=" CA TRP G 57 " pdb=" C TRP G 57 " pdb=" N VAL G 58 " pdb=" CA VAL G 58 " ideal model delta harmonic sigma weight residual -180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA TRP I 57 " pdb=" C TRP I 57 " pdb=" N VAL I 58 " pdb=" CA VAL I 58 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA TRP o 57 " pdb=" C TRP o 57 " pdb=" N VAL o 58 " pdb=" CA VAL o 58 " ideal model delta harmonic sigma weight residual -180.00 -151.11 -28.89 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 13593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3120 0.101 - 0.202: 220 0.202 - 0.303: 24 0.303 - 0.404: 12 0.404 - 0.505: 16 Chirality restraints: 3392 Sorted by residual: chirality pdb=" CA GLU B 349 " pdb=" N GLU B 349 " pdb=" C GLU B 349 " pdb=" CB GLU B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" CA GLU D 349 " pdb=" N GLU D 349 " pdb=" C GLU D 349 " pdb=" CB GLU D 349 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" CA GLU H 349 " pdb=" N GLU H 349 " pdb=" C GLU H 349 " pdb=" CB GLU H 349 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.31e+00 ... (remaining 3389 not shown) Planarity restraints: 3864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY G 100 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C GLY G 100 " 0.048 2.00e-02 2.50e+03 pdb=" O GLY G 100 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN G 101 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 100 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C GLY M 100 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY M 100 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN M 101 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY o 100 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" C GLY o 100 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY o 100 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN o 101 " 0.016 2.00e-02 2.50e+03 ... (remaining 3861 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.70: 659 2.70 - 3.31: 23620 3.31 - 3.92: 41175 3.92 - 4.53: 56357 4.53 - 5.14: 86654 Nonbonded interactions: 208465 Sorted by model distance: nonbonded pdb=" OH TYR F 447 " pdb=" OG1 THR H 441 " model vdw 2.085 2.440 nonbonded pdb=" N ASP B 293 " pdb=" OD1 ASP B 293 " model vdw 2.108 2.520 nonbonded pdb=" N ASP D 293 " pdb=" OD1 ASP D 293 " model vdw 2.109 2.520 nonbonded pdb=" N ASP F 293 " pdb=" OD1 ASP F 293 " model vdw 2.109 2.520 nonbonded pdb=" N ASP H 293 " pdb=" OD1 ASP H 293 " model vdw 2.109 2.520 ... (remaining 208460 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' and resid 208 through 490) selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'M' selection = chain 'o' } ncs_group { reference = chain 'J' selection = chain 'N' selection = chain 'O' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 16.380 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 58.620 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 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 : 0.009 0.219 22548 Z= 0.585 Angle : 1.047 14.051 30552 Z= 0.583 Chirality : 0.067 0.505 3392 Planarity : 0.006 0.064 3864 Dihedral : 14.446 85.149 8480 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.44 % Allowed : 3.85 % Favored : 95.71 % Rotamer: Outliers : 6.01 % Allowed : 7.90 % Favored : 86.08 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 2728 helix: -0.29 (0.12), residues: 1516 sheet: 0.99 (0.38), residues: 196 loop : -2.29 (0.15), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP o 243 HIS 0.009 0.001 HIS I 135 PHE 0.020 0.002 PHE H 296 TYR 0.016 0.002 TYR H 487 ARG 0.004 0.001 ARG F 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 549 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 259 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7132 (m-10) REVERT: D 260 ARG cc_start: 0.5410 (OUTLIER) cc_final: 0.4494 (ttm170) REVERT: D 351 GLN cc_start: 0.4956 (OUTLIER) cc_final: 0.3568 (mp10) REVERT: D 386 ILE cc_start: 0.8061 (mt) cc_final: 0.7821 (mt) REVERT: D 463 LEU cc_start: 0.7066 (mt) cc_final: 0.6740 (mt) REVERT: G 73 MET cc_start: 0.7728 (mtp) cc_final: 0.7476 (mtp) REVERT: G 94 LYS cc_start: 0.6982 (mtpt) cc_final: 0.6654 (mtmm) REVERT: G 104 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7250 (ttmp) REVERT: G 124 LYS cc_start: 0.7357 (mtmt) cc_final: 0.7112 (mtpp) REVERT: G 129 ARG cc_start: 0.7148 (ptm160) cc_final: 0.6797 (ptt-90) REVERT: G 276 LYS cc_start: 0.7739 (tttt) cc_final: 0.7232 (ttmm) REVERT: G 331 MET cc_start: 0.6438 (mmt) cc_final: 0.6200 (mtm) REVERT: I 73 MET cc_start: 0.7570 (mtp) cc_final: 0.7326 (mtp) REVERT: I 94 LYS cc_start: 0.6998 (mtpt) cc_final: 0.6642 (mtmm) REVERT: I 106 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8141 (mtpt) REVERT: I 119 ILE cc_start: 0.8184 (mt) cc_final: 0.7809 (mm) REVERT: I 124 LYS cc_start: 0.7604 (mtmt) cc_final: 0.7381 (mtpp) REVERT: I 129 ARG cc_start: 0.7148 (ptm160) cc_final: 0.6775 (ptt-90) REVERT: I 141 LYS cc_start: 0.7719 (mttt) cc_final: 0.7369 (mttm) REVERT: I 227 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7585 (t) REVERT: I 268 LYS cc_start: 0.8279 (tttt) cc_final: 0.8020 (ttpt) REVERT: I 274 LYS cc_start: 0.7655 (tttt) cc_final: 0.7376 (ttpt) REVERT: I 276 LYS cc_start: 0.7571 (tttt) cc_final: 0.7055 (ttmt) REVERT: I 290 LYS cc_start: 0.6638 (mtmt) cc_final: 0.6390 (mmtp) REVERT: I 331 MET cc_start: 0.6666 (mmt) cc_final: 0.6171 (mtm) REVERT: J 138 ARG cc_start: 0.8203 (ptm160) cc_final: 0.7719 (ptm160) REVERT: J 144 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7572 (mtt90) REVERT: J 170 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7394 (mtt-85) REVERT: J 181 SER cc_start: 0.7683 (t) cc_final: 0.7442 (m) REVERT: M 73 MET cc_start: 0.7747 (mtp) cc_final: 0.7461 (mtp) REVERT: M 94 LYS cc_start: 0.6987 (mtpt) cc_final: 0.6669 (mtmm) REVERT: M 104 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.6773 (ttmp) REVERT: M 124 LYS cc_start: 0.7642 (mtmt) cc_final: 0.7376 (mtpp) REVERT: M 129 ARG cc_start: 0.7301 (ptm160) cc_final: 0.6886 (ptt-90) REVERT: M 141 LYS cc_start: 0.7571 (mttt) cc_final: 0.7170 (mttm) REVERT: M 227 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7731 (t) REVERT: M 268 LYS cc_start: 0.8263 (tttt) cc_final: 0.8034 (ttpt) REVERT: M 274 LYS cc_start: 0.7674 (tttt) cc_final: 0.7431 (ttpt) REVERT: M 276 LYS cc_start: 0.7503 (tttt) cc_final: 0.7007 (ttmt) REVERT: M 331 MET cc_start: 0.6531 (mmt) cc_final: 0.6183 (mtm) REVERT: N 144 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7555 (mtt90) REVERT: N 170 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7372 (mtt-85) REVERT: N 181 SER cc_start: 0.7686 (t) cc_final: 0.7474 (m) REVERT: O 144 ARG cc_start: 0.7840 (mtm180) cc_final: 0.7537 (mtt90) REVERT: O 168 ARG cc_start: 0.8130 (mtm180) cc_final: 0.7827 (mtm-85) REVERT: O 170 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7078 (mmt-90) REVERT: O 181 SER cc_start: 0.7961 (t) cc_final: 0.7617 (m) REVERT: O 199 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6415 (mm-30) REVERT: P 124 GLN cc_start: 0.8299 (mt0) cc_final: 0.8093 (mt0) REVERT: P 144 ARG cc_start: 0.7815 (mtm180) cc_final: 0.7489 (mtt90) REVERT: P 161 TYR cc_start: 0.6559 (t80) cc_final: 0.6161 (t80) REVERT: P 168 ARG cc_start: 0.8022 (mtm180) cc_final: 0.7641 (mtm-85) REVERT: P 170 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7486 (mtt-85) REVERT: o 73 MET cc_start: 0.7579 (mtp) cc_final: 0.7269 (mtp) REVERT: o 94 LYS cc_start: 0.6993 (mtpt) cc_final: 0.6717 (mtmm) REVERT: o 104 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7329 (tppt) REVERT: o 119 ILE cc_start: 0.8203 (mt) cc_final: 0.7856 (mm) REVERT: o 124 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7447 (mtpp) REVERT: o 129 ARG cc_start: 0.7302 (ptm160) cc_final: 0.6838 (ptt-90) REVERT: o 227 VAL cc_start: 0.7794 (OUTLIER) cc_final: 0.7472 (t) REVERT: o 268 LYS cc_start: 0.8240 (tttt) cc_final: 0.7970 (ttpt) REVERT: o 276 LYS cc_start: 0.7401 (tttt) cc_final: 0.6877 (ttmt) REVERT: o 331 MET cc_start: 0.6613 (mmt) cc_final: 0.6227 (mtm) REVERT: B 260 ARG cc_start: 0.5318 (OUTLIER) cc_final: 0.4748 (ttm170) REVERT: B 337 ILE cc_start: 0.6270 (mt) cc_final: 0.5943 (mt) REVERT: B 350 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.6351 (mmt180) REVERT: B 407 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7381 (mm) REVERT: F 259 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6166 (m-10) REVERT: F 463 LEU cc_start: 0.7147 (mt) cc_final: 0.6911 (mt) REVERT: H 244 ILE cc_start: 0.7513 (mt) cc_final: 0.7043 (mt) REVERT: H 301 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5821 (tt) REVERT: H 309 GLU cc_start: 0.3583 (tm-30) cc_final: 0.2885 (tm-30) REVERT: H 341 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9023 (mt) REVERT: H 351 GLN cc_start: 0.5344 (OUTLIER) cc_final: 0.3167 (mp10) REVERT: H 376 LYS cc_start: 0.6759 (mtpp) cc_final: 0.6537 (mtpp) outliers start: 140 outliers final: 43 residues processed: 652 average time/residue: 0.4007 time to fit residues: 378.1157 Evaluate side-chains 509 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 449 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 LYS Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 LYS Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain O residue 199 GLU Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain o residue 104 LYS Chi-restraints excluded: chain o residue 227 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain F residue 259 PHE Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 358 MET Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain H residue 358 MET Chi-restraints excluded: chain H residue 359 SER Chi-restraints excluded: chain H residue 407 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 243 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 329 ASN H 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22548 Z= 0.219 Angle : 0.600 8.678 30552 Z= 0.313 Chirality : 0.042 0.129 3392 Planarity : 0.005 0.045 3864 Dihedral : 11.359 61.522 3411 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.44 % Allowed : 2.64 % Favored : 96.92 % Rotamer: Outliers : 3.05 % Allowed : 11.13 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 2728 helix: 1.01 (0.13), residues: 1500 sheet: 0.29 (0.39), residues: 176 loop : -1.86 (0.15), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 243 HIS 0.008 0.001 HIS G 135 PHE 0.025 0.001 PHE D 314 TYR 0.023 0.002 TYR D 339 ARG 0.006 0.000 ARG D 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 492 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 293 ASP cc_start: 0.3107 (OUTLIER) cc_final: 0.2758 (m-30) REVERT: D 308 PHE cc_start: 0.4778 (t80) cc_final: 0.4401 (t80) REVERT: D 450 MET cc_start: 0.7315 (mtp) cc_final: 0.7112 (mtp) REVERT: G 73 MET cc_start: 0.7516 (mtp) cc_final: 0.7305 (mtp) REVERT: G 94 LYS cc_start: 0.7010 (mtpt) cc_final: 0.6686 (mtmm) REVERT: G 129 ARG cc_start: 0.7257 (ptm160) cc_final: 0.6853 (ptt-90) REVERT: G 141 LYS cc_start: 0.7440 (mttt) cc_final: 0.7084 (mttm) REVERT: G 331 MET cc_start: 0.6366 (mmt) cc_final: 0.6100 (mtm) REVERT: I 73 MET cc_start: 0.7373 (mtp) cc_final: 0.7139 (mtp) REVERT: I 94 LYS cc_start: 0.7077 (mtpt) cc_final: 0.6799 (mtmm) REVERT: I 129 ARG cc_start: 0.7334 (ptm160) cc_final: 0.6861 (ptt-90) REVERT: I 141 LYS cc_start: 0.7434 (mttt) cc_final: 0.7093 (mttm) REVERT: I 268 LYS cc_start: 0.8282 (tttt) cc_final: 0.8021 (ttpt) REVERT: I 274 LYS cc_start: 0.7477 (tttt) cc_final: 0.7261 (ttpt) REVERT: I 276 LYS cc_start: 0.7612 (tttt) cc_final: 0.7033 (ttmt) REVERT: I 331 MET cc_start: 0.6492 (mmt) cc_final: 0.6070 (mtm) REVERT: I 338 GLN cc_start: 0.7022 (mm-40) cc_final: 0.6452 (mm-40) REVERT: J 144 ARG cc_start: 0.7857 (mtm180) cc_final: 0.7640 (mtt90) REVERT: J 170 ARG cc_start: 0.7757 (mtt180) cc_final: 0.7517 (mtt-85) REVERT: M 73 MET cc_start: 0.7452 (mtp) cc_final: 0.7203 (mtp) REVERT: M 94 LYS cc_start: 0.7090 (mtpt) cc_final: 0.6771 (mtmm) REVERT: M 129 ARG cc_start: 0.7406 (ptm160) cc_final: 0.6936 (ptt-90) REVERT: M 141 LYS cc_start: 0.7476 (mttt) cc_final: 0.7132 (mttm) REVERT: M 268 LYS cc_start: 0.8301 (tttt) cc_final: 0.8090 (ttpt) REVERT: M 274 LYS cc_start: 0.7634 (tttt) cc_final: 0.7426 (ttpt) REVERT: M 276 LYS cc_start: 0.7558 (tttt) cc_final: 0.6979 (ttmt) REVERT: M 331 MET cc_start: 0.6405 (mmt) cc_final: 0.6095 (mtm) REVERT: M 338 GLN cc_start: 0.7124 (mm-40) cc_final: 0.6832 (mm-40) REVERT: N 144 ARG cc_start: 0.7892 (mtm180) cc_final: 0.7671 (mtt90) REVERT: N 170 ARG cc_start: 0.7772 (mtt180) cc_final: 0.6956 (mmt-90) REVERT: O 144 ARG cc_start: 0.7915 (mtm180) cc_final: 0.7685 (mtt90) REVERT: O 170 ARG cc_start: 0.7849 (mtt180) cc_final: 0.7069 (mmt-90) REVERT: O 199 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.6260 (mm-30) REVERT: P 144 ARG cc_start: 0.7925 (mtm180) cc_final: 0.7684 (mtt90) REVERT: P 170 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7601 (mtt-85) REVERT: o 73 MET cc_start: 0.7342 (mtp) cc_final: 0.7096 (mtp) REVERT: o 94 LYS cc_start: 0.7066 (mtpt) cc_final: 0.6828 (mtmm) REVERT: o 129 ARG cc_start: 0.7351 (ptm160) cc_final: 0.6850 (ptt-90) REVERT: o 141 LYS cc_start: 0.7463 (mttt) cc_final: 0.7097 (mttm) REVERT: o 268 LYS cc_start: 0.8249 (tttt) cc_final: 0.8003 (ttpt) REVERT: o 276 LYS cc_start: 0.7467 (tttt) cc_final: 0.6896 (ttmt) REVERT: o 331 MET cc_start: 0.6503 (mmt) cc_final: 0.6119 (mtm) REVERT: o 338 GLN cc_start: 0.7036 (mm-40) cc_final: 0.6436 (mm-40) REVERT: B 262 GLU cc_start: 0.5429 (OUTLIER) cc_final: 0.5171 (mt-10) REVERT: B 337 ILE cc_start: 0.6388 (mt) cc_final: 0.6053 (mt) REVERT: H 226 TYR cc_start: 0.5274 (m-80) cc_final: 0.5039 (m-80) outliers start: 71 outliers final: 41 residues processed: 537 average time/residue: 0.4282 time to fit residues: 336.7555 Evaluate side-chains 499 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 455 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain O residue 199 GLU Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain o residue 279 SER Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 407 ILE Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 472 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 243 optimal weight: 9.9990 chunk 263 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 241 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22548 Z= 0.219 Angle : 0.570 7.966 30552 Z= 0.298 Chirality : 0.042 0.145 3392 Planarity : 0.004 0.044 3864 Dihedral : 10.376 65.450 3314 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.44 % Allowed : 3.15 % Favored : 96.41 % Rotamer: Outliers : 3.05 % Allowed : 11.51 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2728 helix: 1.31 (0.14), residues: 1528 sheet: 1.18 (0.37), residues: 196 loop : -1.96 (0.16), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP o 243 HIS 0.007 0.001 HIS M 135 PHE 0.020 0.001 PHE H 315 TYR 0.017 0.001 TYR D 339 ARG 0.004 0.000 ARG F 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 464 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 MET cc_start: 0.7410 (mtp) cc_final: 0.7165 (mtp) REVERT: G 94 LYS cc_start: 0.7088 (mtpt) cc_final: 0.6754 (mtmm) REVERT: G 104 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7284 (tppt) REVERT: G 129 ARG cc_start: 0.7249 (ptm160) cc_final: 0.6830 (ptt-90) REVERT: G 141 LYS cc_start: 0.7440 (mttt) cc_final: 0.7096 (mttm) REVERT: G 331 MET cc_start: 0.6502 (mmt) cc_final: 0.6153 (mtm) REVERT: G 338 GLN cc_start: 0.7124 (mm-40) cc_final: 0.6889 (mm-40) REVERT: I 73 MET cc_start: 0.7382 (mtp) cc_final: 0.7131 (mtp) REVERT: I 94 LYS cc_start: 0.7068 (mtpt) cc_final: 0.6754 (mtmm) REVERT: I 104 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7330 (tppt) REVERT: I 129 ARG cc_start: 0.7285 (ptm160) cc_final: 0.6822 (ptt-90) REVERT: I 141 LYS cc_start: 0.7482 (mttt) cc_final: 0.7125 (mttm) REVERT: I 268 LYS cc_start: 0.8240 (tttt) cc_final: 0.8001 (ttpt) REVERT: I 331 MET cc_start: 0.6507 (mmt) cc_final: 0.6048 (mtm) REVERT: J 144 ARG cc_start: 0.7906 (mtm180) cc_final: 0.7678 (mtt90) REVERT: J 170 ARG cc_start: 0.7786 (mtt180) cc_final: 0.7536 (mtt-85) REVERT: J 195 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6755 (tm-30) REVERT: M 73 MET cc_start: 0.7409 (mtp) cc_final: 0.7135 (mtp) REVERT: M 94 LYS cc_start: 0.7076 (mtpt) cc_final: 0.6761 (mtmm) REVERT: M 104 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7282 (tppt) REVERT: M 129 ARG cc_start: 0.7313 (ptm160) cc_final: 0.6828 (ptt-90) REVERT: M 141 LYS cc_start: 0.7501 (mttt) cc_final: 0.7130 (mttm) REVERT: M 268 LYS cc_start: 0.8315 (tttt) cc_final: 0.8115 (ttpt) REVERT: M 276 LYS cc_start: 0.7563 (tttt) cc_final: 0.6978 (ttmt) REVERT: M 331 MET cc_start: 0.6466 (mmt) cc_final: 0.6085 (mtm) REVERT: N 144 ARG cc_start: 0.7939 (mtm180) cc_final: 0.7716 (mtt90) REVERT: N 170 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7021 (mmt-90) REVERT: O 144 ARG cc_start: 0.7974 (mtm180) cc_final: 0.7729 (mtt90) REVERT: O 170 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7076 (mmt-90) REVERT: O 199 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6107 (mm-30) REVERT: P 144 ARG cc_start: 0.7966 (mtm180) cc_final: 0.7724 (mtt90) REVERT: P 170 ARG cc_start: 0.7802 (mtt180) cc_final: 0.7570 (mtt-85) REVERT: o 73 MET cc_start: 0.7374 (mtp) cc_final: 0.7095 (mtp) REVERT: o 94 LYS cc_start: 0.7096 (mtpt) cc_final: 0.6808 (mtmm) REVERT: o 129 ARG cc_start: 0.7274 (ptm160) cc_final: 0.6781 (ptt-90) REVERT: o 141 LYS cc_start: 0.7486 (mttt) cc_final: 0.7127 (mttm) REVERT: o 268 LYS cc_start: 0.8282 (tttt) cc_final: 0.8061 (ttpt) REVERT: o 276 LYS cc_start: 0.7503 (tttt) cc_final: 0.6914 (ttmt) REVERT: o 331 MET cc_start: 0.6523 (mmt) cc_final: 0.6101 (mtm) REVERT: F 442 MET cc_start: 0.6605 (mtm) cc_final: 0.6390 (mtp) outliers start: 71 outliers final: 42 residues processed: 513 average time/residue: 0.3994 time to fit residues: 298.5876 Evaluate side-chains 489 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 443 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain G residue 104 LYS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain I residue 104 LYS Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 199 GLU Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain o residue 154 VAL Chi-restraints excluded: chain o residue 279 SER Chi-restraints excluded: chain o residue 346 SER Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 472 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 1.9990 chunk 183 optimal weight: 0.3980 chunk 126 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 163 optimal weight: 0.4980 chunk 244 optimal weight: 2.9990 chunk 259 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 231 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 124 GLN B 451 HIS F 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22548 Z= 0.151 Angle : 0.509 8.475 30552 Z= 0.264 Chirality : 0.040 0.119 3392 Planarity : 0.004 0.044 3864 Dihedral : 9.453 59.603 3294 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.68 % Favored : 97.03 % Rotamer: Outliers : 2.62 % Allowed : 12.16 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.16), residues: 2728 helix: 1.51 (0.14), residues: 1552 sheet: 0.72 (0.41), residues: 156 loop : -1.58 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP o 243 HIS 0.005 0.001 HIS M 135 PHE 0.019 0.001 PHE H 315 TYR 0.016 0.001 TYR D 339 ARG 0.003 0.000 ARG H 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 454 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 MET cc_start: 0.7389 (mtp) cc_final: 0.7119 (mtp) REVERT: G 94 LYS cc_start: 0.7071 (mtpt) cc_final: 0.6720 (mtmm) REVERT: G 129 ARG cc_start: 0.7207 (ptm160) cc_final: 0.6767 (ptt-90) REVERT: G 141 LYS cc_start: 0.7491 (mttt) cc_final: 0.7138 (mttm) REVERT: G 331 MET cc_start: 0.6519 (mmt) cc_final: 0.6146 (mtm) REVERT: I 73 MET cc_start: 0.7366 (mtp) cc_final: 0.7123 (mtp) REVERT: I 94 LYS cc_start: 0.7079 (mtpt) cc_final: 0.6752 (mtmm) REVERT: I 129 ARG cc_start: 0.7255 (ptm160) cc_final: 0.6781 (ptt-90) REVERT: I 141 LYS cc_start: 0.7488 (mttt) cc_final: 0.7132 (mttm) REVERT: I 268 LYS cc_start: 0.8227 (tttt) cc_final: 0.7997 (ttpt) REVERT: I 331 MET cc_start: 0.6569 (mmt) cc_final: 0.6145 (mtm) REVERT: I 338 GLN cc_start: 0.7000 (mm-40) cc_final: 0.6525 (mm-40) REVERT: J 170 ARG cc_start: 0.7777 (mtt180) cc_final: 0.7565 (mtt-85) REVERT: M 73 MET cc_start: 0.7371 (mtp) cc_final: 0.7104 (mtp) REVERT: M 94 LYS cc_start: 0.7098 (mtpt) cc_final: 0.6767 (mtmm) REVERT: M 129 ARG cc_start: 0.7262 (ptm160) cc_final: 0.6772 (ptt-90) REVERT: M 141 LYS cc_start: 0.7469 (mttt) cc_final: 0.7119 (mttm) REVERT: M 268 LYS cc_start: 0.8300 (tttt) cc_final: 0.8094 (ttpt) REVERT: M 331 MET cc_start: 0.6519 (mmt) cc_final: 0.6124 (mtm) REVERT: N 144 ARG cc_start: 0.7936 (mtm180) cc_final: 0.7727 (mtt90) REVERT: N 170 ARG cc_start: 0.7786 (mtt180) cc_final: 0.7547 (mtt-85) REVERT: O 144 ARG cc_start: 0.7939 (mtm180) cc_final: 0.7718 (mtt90) REVERT: O 170 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7599 (mtt-85) REVERT: O 199 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.6059 (mm-30) REVERT: P 144 ARG cc_start: 0.7926 (mtm180) cc_final: 0.7712 (mtt90) REVERT: P 170 ARG cc_start: 0.7776 (mtt180) cc_final: 0.7573 (mtt-85) REVERT: o 73 MET cc_start: 0.7352 (mtp) cc_final: 0.7100 (mtp) REVERT: o 94 LYS cc_start: 0.7069 (mtpt) cc_final: 0.6748 (mtmm) REVERT: o 104 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7275 (tppt) REVERT: o 129 ARG cc_start: 0.7247 (ptm160) cc_final: 0.6756 (ptt-90) REVERT: o 141 LYS cc_start: 0.7469 (mttt) cc_final: 0.7130 (mttm) REVERT: o 331 MET cc_start: 0.6591 (mmt) cc_final: 0.6173 (mtm) REVERT: o 338 GLN cc_start: 0.6945 (mm-40) cc_final: 0.6553 (mm-40) REVERT: H 333 ILE cc_start: 0.6671 (mm) cc_final: 0.6441 (mm) outliers start: 61 outliers final: 44 residues processed: 489 average time/residue: 0.3949 time to fit residues: 281.0182 Evaluate side-chains 490 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 444 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 295 ILE Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 199 GLU Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain o residue 104 LYS Chi-restraints excluded: chain o residue 279 SER Chi-restraints excluded: chain o residue 346 SER Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 488 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 232 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 124 GLN O 124 GLN P 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22548 Z= 0.212 Angle : 0.541 7.189 30552 Z= 0.280 Chirality : 0.041 0.123 3392 Planarity : 0.004 0.046 3864 Dihedral : 9.691 62.897 3294 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.44 % Allowed : 3.30 % Favored : 96.26 % Rotamer: Outliers : 2.75 % Allowed : 12.29 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2728 helix: 1.51 (0.14), residues: 1556 sheet: 0.91 (0.35), residues: 216 loop : -1.67 (0.17), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP o 243 HIS 0.006 0.001 HIS M 135 PHE 0.023 0.001 PHE F 406 TYR 0.013 0.001 TYR D 339 ARG 0.006 0.000 ARG J 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 446 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 MET cc_start: 0.7414 (mtp) cc_final: 0.7119 (mtp) REVERT: G 94 LYS cc_start: 0.7104 (mtpt) cc_final: 0.6752 (mtmm) REVERT: G 129 ARG cc_start: 0.7261 (ptm160) cc_final: 0.6814 (ptt-90) REVERT: G 141 LYS cc_start: 0.7474 (mttt) cc_final: 0.7125 (mttm) REVERT: G 331 MET cc_start: 0.6551 (mmt) cc_final: 0.6155 (mtm) REVERT: I 73 MET cc_start: 0.7396 (mtp) cc_final: 0.7127 (mtp) REVERT: I 94 LYS cc_start: 0.7073 (mtpt) cc_final: 0.6728 (mtmm) REVERT: I 129 ARG cc_start: 0.7293 (ptm160) cc_final: 0.6814 (ptt-90) REVERT: I 141 LYS cc_start: 0.7485 (mttt) cc_final: 0.7135 (mttm) REVERT: I 268 LYS cc_start: 0.8228 (tttt) cc_final: 0.7997 (ttpt) REVERT: I 331 MET cc_start: 0.6530 (mmt) cc_final: 0.6089 (mtm) REVERT: M 73 MET cc_start: 0.7400 (mtp) cc_final: 0.7119 (mtp) REVERT: M 94 LYS cc_start: 0.7133 (mtpt) cc_final: 0.6798 (mtmm) REVERT: M 129 ARG cc_start: 0.7314 (ptm160) cc_final: 0.6816 (ptt-90) REVERT: M 141 LYS cc_start: 0.7485 (mttt) cc_final: 0.7127 (mttm) REVERT: M 331 MET cc_start: 0.6529 (mmt) cc_final: 0.6135 (mtm) REVERT: N 144 ARG cc_start: 0.7957 (mtm180) cc_final: 0.7752 (mtt90) REVERT: N 170 ARG cc_start: 0.7821 (mtt180) cc_final: 0.7031 (mmt-90) REVERT: O 124 GLN cc_start: 0.8185 (mt0) cc_final: 0.7916 (mt0) REVERT: O 144 ARG cc_start: 0.7969 (mtm180) cc_final: 0.7752 (mtt90) REVERT: O 199 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.6060 (mm-30) REVERT: P 144 ARG cc_start: 0.7950 (mtm180) cc_final: 0.7736 (mtt90) REVERT: o 73 MET cc_start: 0.7380 (mtp) cc_final: 0.7109 (mtp) REVERT: o 94 LYS cc_start: 0.7066 (mtpt) cc_final: 0.6727 (mtmm) REVERT: o 104 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7341 (tppt) REVERT: o 129 ARG cc_start: 0.7310 (ptm160) cc_final: 0.6799 (ptt-90) REVERT: o 141 LYS cc_start: 0.7482 (mttt) cc_final: 0.7134 (mttm) REVERT: o 331 MET cc_start: 0.6551 (mmt) cc_final: 0.6129 (mtm) REVERT: B 364 ARG cc_start: 0.6014 (ttp-170) cc_final: 0.5643 (ttt-90) outliers start: 64 outliers final: 49 residues processed: 486 average time/residue: 0.3989 time to fit residues: 283.2867 Evaluate side-chains 493 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 442 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 488 HIS Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 199 GLU Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain o residue 104 LYS Chi-restraints excluded: chain o residue 279 SER Chi-restraints excluded: chain o residue 346 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 407 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 472 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 0.6980 chunk 233 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 215 optimal weight: 0.1980 chunk 120 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 124 GLN N 124 GLN P 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22548 Z= 0.191 Angle : 0.523 7.512 30552 Z= 0.271 Chirality : 0.040 0.121 3392 Planarity : 0.004 0.045 3864 Dihedral : 9.502 61.992 3292 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.44 % Allowed : 2.57 % Favored : 96.99 % Rotamer: Outliers : 3.01 % Allowed : 12.46 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 2728 helix: 1.57 (0.14), residues: 1556 sheet: 0.39 (0.38), residues: 176 loop : -1.46 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 243 HIS 0.006 0.001 HIS o 135 PHE 0.020 0.001 PHE F 406 TYR 0.013 0.001 TYR D 339 ARG 0.009 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 445 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 40 ARG cc_start: 0.7877 (ptp-170) cc_final: 0.7532 (ptp-170) REVERT: G 73 MET cc_start: 0.7401 (mtp) cc_final: 0.7115 (mtp) REVERT: G 94 LYS cc_start: 0.7108 (mtpt) cc_final: 0.6743 (mtmm) REVERT: G 129 ARG cc_start: 0.7253 (ptm160) cc_final: 0.6783 (ptt-90) REVERT: G 141 LYS cc_start: 0.7479 (mttt) cc_final: 0.7129 (mttm) REVERT: G 331 MET cc_start: 0.6549 (mmt) cc_final: 0.6163 (mtm) REVERT: I 40 ARG cc_start: 0.7858 (ptp-170) cc_final: 0.7449 (ptp-170) REVERT: I 73 MET cc_start: 0.7393 (mtp) cc_final: 0.7105 (mtp) REVERT: I 94 LYS cc_start: 0.7085 (mtpt) cc_final: 0.6721 (mtmm) REVERT: I 129 ARG cc_start: 0.7252 (ptm160) cc_final: 0.6785 (ptt-90) REVERT: I 141 LYS cc_start: 0.7486 (mttt) cc_final: 0.7137 (mttm) REVERT: I 268 LYS cc_start: 0.8257 (tttt) cc_final: 0.8026 (ttpt) REVERT: I 331 MET cc_start: 0.6542 (mmt) cc_final: 0.6084 (mtm) REVERT: M 40 ARG cc_start: 0.7807 (ptp-170) cc_final: 0.7441 (ptp-170) REVERT: M 73 MET cc_start: 0.7385 (mtp) cc_final: 0.7073 (mtp) REVERT: M 94 LYS cc_start: 0.7106 (mtpt) cc_final: 0.6732 (mtmm) REVERT: M 129 ARG cc_start: 0.7303 (ptm160) cc_final: 0.6808 (ptt-90) REVERT: M 141 LYS cc_start: 0.7487 (mttt) cc_final: 0.7139 (mttm) REVERT: M 331 MET cc_start: 0.6510 (mmt) cc_final: 0.6118 (mtm) REVERT: N 124 GLN cc_start: 0.8138 (mt0) cc_final: 0.7888 (mt0) REVERT: N 144 ARG cc_start: 0.7959 (mtm180) cc_final: 0.7751 (mtt90) REVERT: N 170 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7036 (mmt-90) REVERT: O 124 GLN cc_start: 0.8181 (mt0) cc_final: 0.7946 (mt0) REVERT: O 144 ARG cc_start: 0.7973 (mtm180) cc_final: 0.7750 (mtt90) REVERT: O 199 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.6041 (mm-30) REVERT: P 144 ARG cc_start: 0.7951 (mtm180) cc_final: 0.7736 (mtt90) REVERT: o 40 ARG cc_start: 0.7905 (ptp-170) cc_final: 0.7510 (ptp-170) REVERT: o 73 MET cc_start: 0.7379 (mtp) cc_final: 0.7075 (mtp) REVERT: o 94 LYS cc_start: 0.7089 (mtpt) cc_final: 0.6722 (mtmm) REVERT: o 104 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7306 (tppt) REVERT: o 129 ARG cc_start: 0.7264 (ptm160) cc_final: 0.6775 (ptt-90) REVERT: o 141 LYS cc_start: 0.7485 (mttt) cc_final: 0.7139 (mttm) REVERT: o 331 MET cc_start: 0.6560 (mmt) cc_final: 0.6149 (mtm) REVERT: B 364 ARG cc_start: 0.5799 (ttp-170) cc_final: 0.5501 (ttt-90) outliers start: 70 outliers final: 62 residues processed: 492 average time/residue: 0.3804 time to fit residues: 273.8344 Evaluate side-chains 500 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 436 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 488 HIS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 199 GLU Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain o residue 104 LYS Chi-restraints excluded: chain o residue 154 VAL Chi-restraints excluded: chain o residue 279 SER Chi-restraints excluded: chain o residue 295 ILE Chi-restraints excluded: chain o residue 346 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 407 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 472 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 189 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 124 GLN P 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22548 Z= 0.352 Angle : 0.623 8.793 30552 Z= 0.325 Chirality : 0.045 0.132 3392 Planarity : 0.005 0.048 3864 Dihedral : 10.419 69.724 3292 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.07 % Favored : 95.49 % Rotamer: Outliers : 3.22 % Allowed : 12.80 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2728 helix: 1.32 (0.14), residues: 1552 sheet: 0.80 (0.36), residues: 212 loop : -1.65 (0.17), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 57 HIS 0.007 0.001 HIS I 135 PHE 0.019 0.002 PHE F 406 TYR 0.015 0.002 TYR I 270 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 443 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 40 ARG cc_start: 0.7932 (ptp-170) cc_final: 0.7557 (ptp-170) REVERT: G 73 MET cc_start: 0.7459 (mtp) cc_final: 0.7148 (mtp) REVERT: G 94 LYS cc_start: 0.7246 (mtpt) cc_final: 0.6870 (mtmm) REVERT: G 129 ARG cc_start: 0.7280 (ptm160) cc_final: 0.6853 (ptt-90) REVERT: G 141 LYS cc_start: 0.7488 (mttt) cc_final: 0.7093 (mttm) REVERT: G 331 MET cc_start: 0.6544 (mmt) cc_final: 0.6128 (mtm) REVERT: G 338 GLN cc_start: 0.7096 (mm-40) cc_final: 0.6878 (mm-40) REVERT: I 73 MET cc_start: 0.7461 (mtp) cc_final: 0.7166 (mtp) REVERT: I 94 LYS cc_start: 0.7216 (mtpt) cc_final: 0.6852 (mtmm) REVERT: I 129 ARG cc_start: 0.7284 (ptm160) cc_final: 0.6835 (ptt-90) REVERT: I 141 LYS cc_start: 0.7500 (mttt) cc_final: 0.7110 (mttm) REVERT: I 268 LYS cc_start: 0.8275 (tttt) cc_final: 0.8038 (ttpt) REVERT: I 331 MET cc_start: 0.6515 (mmt) cc_final: 0.6080 (mtm) REVERT: M 40 ARG cc_start: 0.7848 (ptp-170) cc_final: 0.7488 (ptp-170) REVERT: M 73 MET cc_start: 0.7442 (mtp) cc_final: 0.7135 (mtp) REVERT: M 94 LYS cc_start: 0.7230 (mtpt) cc_final: 0.6861 (mtmm) REVERT: M 129 ARG cc_start: 0.7312 (ptm160) cc_final: 0.6851 (ptt-90) REVERT: M 141 LYS cc_start: 0.7502 (mttt) cc_final: 0.7115 (mttm) REVERT: M 331 MET cc_start: 0.6521 (mmt) cc_final: 0.6096 (mtm) REVERT: N 144 ARG cc_start: 0.8014 (mtm180) cc_final: 0.7797 (mtt90) REVERT: O 144 ARG cc_start: 0.8005 (mtm180) cc_final: 0.7779 (mtt90) REVERT: O 199 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6223 (mm-30) REVERT: P 144 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7770 (mtt90) REVERT: o 40 ARG cc_start: 0.7920 (ptp-170) cc_final: 0.7582 (ptp-170) REVERT: o 73 MET cc_start: 0.7446 (mtp) cc_final: 0.7152 (mtp) REVERT: o 94 LYS cc_start: 0.7217 (mtpt) cc_final: 0.6851 (mtmm) REVERT: o 129 ARG cc_start: 0.7268 (ptm160) cc_final: 0.6809 (ptt-90) REVERT: o 141 LYS cc_start: 0.7493 (mttt) cc_final: 0.7104 (mttm) REVERT: o 331 MET cc_start: 0.6544 (mmt) cc_final: 0.6120 (mtm) REVERT: H 376 LYS cc_start: 0.7117 (mtpt) cc_final: 0.6763 (mtpp) REVERT: H 391 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6549 (mp) outliers start: 75 outliers final: 64 residues processed: 492 average time/residue: 0.3875 time to fit residues: 279.0127 Evaluate side-chains 495 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 429 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 199 GLU Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain o residue 154 VAL Chi-restraints excluded: chain o residue 279 SER Chi-restraints excluded: chain o residue 346 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 391 LEU Chi-restraints excluded: chain H residue 407 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 472 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 203 optimal weight: 0.9990 chunk 234 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 124 GLN O 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22548 Z= 0.187 Angle : 0.531 9.665 30552 Z= 0.276 Chirality : 0.041 0.121 3392 Planarity : 0.004 0.047 3864 Dihedral : 9.731 63.696 3292 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.40 % Allowed : 2.75 % Favored : 96.85 % Rotamer: Outliers : 2.96 % Allowed : 13.23 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2728 helix: 1.52 (0.14), residues: 1552 sheet: 0.42 (0.38), residues: 176 loop : -1.46 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 243 HIS 0.006 0.001 HIS o 135 PHE 0.022 0.001 PHE F 406 TYR 0.012 0.001 TYR D 339 ARG 0.008 0.000 ARG N 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 442 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 40 ARG cc_start: 0.7862 (ptp-170) cc_final: 0.7556 (ptp-170) REVERT: G 73 MET cc_start: 0.7399 (mtp) cc_final: 0.7089 (mtp) REVERT: G 94 LYS cc_start: 0.7148 (mtpt) cc_final: 0.6780 (mtmm) REVERT: G 129 ARG cc_start: 0.7217 (ptm160) cc_final: 0.6753 (ptt-90) REVERT: G 141 LYS cc_start: 0.7502 (mttt) cc_final: 0.7144 (mttm) REVERT: G 331 MET cc_start: 0.6513 (mmt) cc_final: 0.6083 (mtm) REVERT: G 338 GLN cc_start: 0.7073 (mm-40) cc_final: 0.6867 (mm-40) REVERT: I 73 MET cc_start: 0.7389 (mtp) cc_final: 0.7082 (mtp) REVERT: I 94 LYS cc_start: 0.7179 (mtpt) cc_final: 0.6817 (mtmm) REVERT: I 129 ARG cc_start: 0.7204 (ptm160) cc_final: 0.6764 (ptt-90) REVERT: I 141 LYS cc_start: 0.7515 (mttt) cc_final: 0.7159 (mttm) REVERT: I 268 LYS cc_start: 0.8272 (tttt) cc_final: 0.8052 (ttpt) REVERT: I 331 MET cc_start: 0.6515 (mmt) cc_final: 0.6022 (mtm) REVERT: M 40 ARG cc_start: 0.7771 (ptp-170) cc_final: 0.7502 (ptp-170) REVERT: M 73 MET cc_start: 0.7382 (mtp) cc_final: 0.7070 (mtp) REVERT: M 94 LYS cc_start: 0.7129 (mtpt) cc_final: 0.6764 (mtmm) REVERT: M 129 ARG cc_start: 0.7235 (ptm160) cc_final: 0.6778 (ptt-90) REVERT: M 141 LYS cc_start: 0.7518 (mttt) cc_final: 0.7165 (mttm) REVERT: M 331 MET cc_start: 0.6500 (mmt) cc_final: 0.6054 (mtm) REVERT: O 124 GLN cc_start: 0.8212 (mt0) cc_final: 0.7996 (mt0) REVERT: O 144 ARG cc_start: 0.7957 (mtm180) cc_final: 0.7746 (mtt90) REVERT: P 144 ARG cc_start: 0.7948 (mtm180) cc_final: 0.7746 (mtt90) REVERT: o 40 ARG cc_start: 0.7849 (ptp-170) cc_final: 0.7584 (ptp-170) REVERT: o 73 MET cc_start: 0.7379 (mtp) cc_final: 0.7102 (mtp) REVERT: o 94 LYS cc_start: 0.7134 (mtpt) cc_final: 0.6772 (mtmm) REVERT: o 129 ARG cc_start: 0.7193 (ptm160) cc_final: 0.6739 (ptt-90) REVERT: o 141 LYS cc_start: 0.7510 (mttt) cc_final: 0.7156 (mttm) REVERT: o 331 MET cc_start: 0.6547 (mmt) cc_final: 0.6068 (mtm) REVERT: H 376 LYS cc_start: 0.7001 (mtpt) cc_final: 0.6715 (mtpp) outliers start: 69 outliers final: 60 residues processed: 482 average time/residue: 0.4014 time to fit residues: 285.8972 Evaluate side-chains 496 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 436 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 488 HIS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 178 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 178 ASP Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain o residue 154 VAL Chi-restraints excluded: chain o residue 279 SER Chi-restraints excluded: chain o residue 295 ILE Chi-restraints excluded: chain o residue 346 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 472 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 0.0170 chunk 225 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 217 optimal weight: 0.5980 chunk 227 optimal weight: 0.6980 chunk 239 optimal weight: 0.4980 chunk 158 optimal weight: 0.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 124 GLN H 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22548 Z= 0.147 Angle : 0.504 9.787 30552 Z= 0.259 Chirality : 0.039 0.120 3392 Planarity : 0.004 0.046 3864 Dihedral : 8.924 58.761 3289 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.86 % Favored : 96.88 % Rotamer: Outliers : 2.23 % Allowed : 14.22 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 2728 helix: 1.63 (0.14), residues: 1576 sheet: 0.74 (0.41), residues: 156 loop : -1.46 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 185 HIS 0.004 0.001 HIS G 135 PHE 0.022 0.001 PHE F 406 TYR 0.011 0.001 TYR D 339 ARG 0.009 0.000 ARG J 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 459 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 MET cc_start: 0.7364 (mtp) cc_final: 0.7064 (mtp) REVERT: G 94 LYS cc_start: 0.7097 (mtpt) cc_final: 0.6729 (mtmm) REVERT: G 129 ARG cc_start: 0.7165 (ptm160) cc_final: 0.6695 (ptt-90) REVERT: G 141 LYS cc_start: 0.7478 (mttt) cc_final: 0.7154 (mttm) REVERT: G 331 MET cc_start: 0.6503 (mmt) cc_final: 0.6075 (mtm) REVERT: G 338 GLN cc_start: 0.7081 (mm-40) cc_final: 0.6647 (mm-40) REVERT: I 73 MET cc_start: 0.7352 (mtp) cc_final: 0.7079 (mtp) REVERT: I 94 LYS cc_start: 0.7156 (mtpt) cc_final: 0.6793 (mtmm) REVERT: I 129 ARG cc_start: 0.7168 (ptm160) cc_final: 0.6714 (ptt-90) REVERT: I 141 LYS cc_start: 0.7493 (mttt) cc_final: 0.7068 (mttm) REVERT: I 268 LYS cc_start: 0.8270 (tttt) cc_final: 0.8065 (ttpt) REVERT: I 331 MET cc_start: 0.6490 (mmt) cc_final: 0.6052 (mtm) REVERT: M 73 MET cc_start: 0.7346 (mtp) cc_final: 0.7046 (mtp) REVERT: M 94 LYS cc_start: 0.7090 (mtpt) cc_final: 0.6728 (mtmm) REVERT: M 129 ARG cc_start: 0.7199 (ptm160) cc_final: 0.6731 (ptt-90) REVERT: M 141 LYS cc_start: 0.7495 (mttt) cc_final: 0.7174 (mttm) REVERT: M 331 MET cc_start: 0.6496 (mmt) cc_final: 0.6032 (mtm) REVERT: O 144 ARG cc_start: 0.7885 (mtm180) cc_final: 0.7684 (mtt90) REVERT: O 199 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6396 (mm-30) REVERT: o 73 MET cc_start: 0.7348 (mtp) cc_final: 0.7070 (mtp) REVERT: o 94 LYS cc_start: 0.7159 (mtpt) cc_final: 0.6808 (mtmm) REVERT: o 129 ARG cc_start: 0.7132 (ptm160) cc_final: 0.6686 (ptt-90) REVERT: o 141 LYS cc_start: 0.7489 (mttt) cc_final: 0.7166 (mttm) REVERT: o 331 MET cc_start: 0.6520 (mmt) cc_final: 0.6089 (mtm) outliers start: 52 outliers final: 50 residues processed: 483 average time/residue: 0.3889 time to fit residues: 275.3283 Evaluate side-chains 492 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 442 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 488 HIS Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 295 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 178 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 178 ASP Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain o residue 295 ILE Chi-restraints excluded: chain o residue 346 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 472 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 266 optimal weight: 0.5980 chunk 245 optimal weight: 0.5980 chunk 212 optimal weight: 0.0570 chunk 22 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 124 GLN P 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22548 Z= 0.147 Angle : 0.505 9.856 30552 Z= 0.260 Chirality : 0.039 0.126 3392 Planarity : 0.004 0.046 3864 Dihedral : 8.731 59.246 3288 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.79 % Favored : 96.96 % Rotamer: Outliers : 2.06 % Allowed : 14.82 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.16), residues: 2728 helix: 1.68 (0.14), residues: 1580 sheet: 0.50 (0.41), residues: 152 loop : -1.31 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 243 HIS 0.005 0.001 HIS G 135 PHE 0.026 0.001 PHE D 308 TYR 0.011 0.001 TYR D 339 ARG 0.007 0.000 ARG J 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 447 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 73 MET cc_start: 0.7381 (mtp) cc_final: 0.7086 (mtp) REVERT: G 94 LYS cc_start: 0.7127 (mtpt) cc_final: 0.6763 (mtmm) REVERT: G 129 ARG cc_start: 0.7236 (ptm160) cc_final: 0.6728 (ptt-90) REVERT: G 141 LYS cc_start: 0.7496 (mttt) cc_final: 0.7047 (mttm) REVERT: G 331 MET cc_start: 0.6486 (mmt) cc_final: 0.6064 (mtm) REVERT: G 338 GLN cc_start: 0.6974 (mm-40) cc_final: 0.6528 (mm-40) REVERT: I 40 ARG cc_start: 0.7625 (ptp-170) cc_final: 0.7351 (ptp-170) REVERT: I 73 MET cc_start: 0.7373 (mtp) cc_final: 0.7105 (mtp) REVERT: I 94 LYS cc_start: 0.7144 (mtpt) cc_final: 0.6795 (mtmm) REVERT: I 129 ARG cc_start: 0.7216 (ptm160) cc_final: 0.6723 (ptt-90) REVERT: I 141 LYS cc_start: 0.7509 (mttt) cc_final: 0.7151 (mttm) REVERT: I 268 LYS cc_start: 0.8284 (tttt) cc_final: 0.8082 (ttpt) REVERT: I 331 MET cc_start: 0.6457 (mmt) cc_final: 0.5994 (mtm) REVERT: M 73 MET cc_start: 0.7366 (mtp) cc_final: 0.7072 (mtp) REVERT: M 94 LYS cc_start: 0.7136 (mtpt) cc_final: 0.6779 (mtmm) REVERT: M 129 ARG cc_start: 0.7230 (ptm160) cc_final: 0.6740 (ptt-90) REVERT: M 141 LYS cc_start: 0.7510 (mttt) cc_final: 0.7149 (mttm) REVERT: M 331 MET cc_start: 0.6474 (mmt) cc_final: 0.6040 (mtm) REVERT: O 199 GLU cc_start: 0.6665 (mm-30) cc_final: 0.6220 (mm-30) REVERT: o 73 MET cc_start: 0.7358 (mtp) cc_final: 0.7091 (mtp) REVERT: o 94 LYS cc_start: 0.7126 (mtpt) cc_final: 0.6790 (mtmm) REVERT: o 129 ARG cc_start: 0.7141 (ptm160) cc_final: 0.6679 (ptt-90) REVERT: o 141 LYS cc_start: 0.7501 (mttt) cc_final: 0.7143 (mttm) REVERT: o 331 MET cc_start: 0.6484 (mmt) cc_final: 0.6047 (mtm) outliers start: 48 outliers final: 48 residues processed: 469 average time/residue: 0.3966 time to fit residues: 272.5367 Evaluate side-chains 490 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 442 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 488 HIS Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 295 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 178 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 178 ASP Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain o residue 295 ILE Chi-restraints excluded: chain o residue 346 SER Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 472 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 212 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 124 GLN P 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.141516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.113407 restraints weight = 27236.712| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.41 r_work: 0.2793 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22548 Z= 0.271 Angle : 0.580 9.612 30552 Z= 0.302 Chirality : 0.043 0.125 3392 Planarity : 0.004 0.046 3864 Dihedral : 9.760 64.734 3288 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.30 % Favored : 96.30 % Rotamer: Outliers : 2.53 % Allowed : 14.52 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2728 helix: 1.53 (0.14), residues: 1552 sheet: 0.82 (0.36), residues: 212 loop : -1.50 (0.17), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP o 57 HIS 0.007 0.001 HIS o 135 PHE 0.021 0.001 PHE F 406 TYR 0.012 0.002 TYR o 270 ARG 0.007 0.000 ARG P 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5654.30 seconds wall clock time: 102 minutes 7.16 seconds (6127.16 seconds total)