Starting phenix.real_space_refine on Fri Mar 22 13:38:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/03_2024/8v89_43031_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/03_2024/8v89_43031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/03_2024/8v89_43031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/03_2024/8v89_43031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/03_2024/8v89_43031_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v89_43031/03_2024/8v89_43031_trim_updated.pdb" } resolution = 2.53 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= 0.000 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 S 115 5.16 5 C 11030 2.51 5 N 2615 2.21 5 O 3105 1.98 5 H 15855 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 70": "OE1" <-> "OE2" Residue "A ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32725 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6400 Chain: "B" Number of atoms: 6365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6400 Chain: "C" Number of atoms: 6365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6400 Chain: "D" Number of atoms: 6365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6400 Chain: "E" Number of atoms: 6365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6400 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'9Z9': 1, 'NAG': 1, 'POV': 1, 'R16': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 26.37, per 1000 atoms: 0.81 Number of scatterers: 32725 At special positions: 0 Unit cell: (98.175, 99, 164.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 115 16.00 P 5 15.00 O 3105 8.00 N 2615 7.00 C 11030 6.00 H 15855 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.04 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.04 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.04 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 67 " " NAG B 602 " - " ASN B 67 " " NAG C 602 " - " ASN C 67 " " NAG D 602 " - " ASN D 67 " " NAG E 602 " - " ASN E 67 " " NAG F 1 " - " ASN A 23 " " NAG G 1 " - " ASN A 110 " " NAG H 1 " - " ASN B 23 " " NAG I 1 " - " ASN B 110 " " NAG J 1 " - " ASN C 23 " " NAG K 1 " - " ASN C 110 " " NAG L 1 " - " ASN D 23 " " NAG M 1 " - " ASN D 110 " " NAG N 1 " - " ASN E 23 " " NAG O 1 " - " ASN E 110 " Time building additional restraints: 26.39 Conformation dependent library (CDL) restraints added in 6.7 seconds 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 25 sheets defined 40.4% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.44 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 215 through 230 removed outlier: 3.859A pdb=" N LEU A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 259 removed outlier: 3.619A pdb=" N LEU A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 295 Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 409 through 465 Processing helix chain 'A' and resid 470 through 477 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 215 through 230 removed outlier: 3.859A pdb=" N LEU B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 259 removed outlier: 3.619A pdb=" N LEU B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 295 Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 409 through 465 Processing helix chain 'B' and resid 470 through 477 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 215 through 230 removed outlier: 3.859A pdb=" N LEU C 226 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 259 removed outlier: 3.619A pdb=" N LEU C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 295 Processing helix chain 'C' and resid 306 through 313 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 409 through 465 Processing helix chain 'C' and resid 470 through 477 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 215 through 230 removed outlier: 3.860A pdb=" N LEU D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 259 removed outlier: 3.619A pdb=" N LEU D 254 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 295 Processing helix chain 'D' and resid 306 through 313 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 409 through 465 Processing helix chain 'D' and resid 470 through 477 Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 215 through 230 removed outlier: 3.859A pdb=" N LEU E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU E 230 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 259 removed outlier: 3.619A pdb=" N LEU E 254 " --> pdb=" O THR E 250 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE E 259 " --> pdb=" O LEU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 295 Processing helix chain 'E' and resid 306 through 313 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 409 through 465 Processing helix chain 'E' and resid 470 through 477 Processing sheet with id= A, first strand: chain 'A' and resid 155 through 159 removed outlier: 6.105A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 41 through 43 Processing sheet with id= C, first strand: chain 'A' and resid 57 through 60 Processing sheet with id= D, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= E, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.527A pdb=" N GLY A 177 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG A 204 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU A 175 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 155 through 159 removed outlier: 6.105A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 41 through 43 Processing sheet with id= H, first strand: chain 'B' and resid 57 through 60 Processing sheet with id= I, first strand: chain 'B' and resid 76 through 79 Processing sheet with id= J, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.528A pdb=" N GLY B 177 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG B 204 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU B 175 " --> pdb=" O ARG B 204 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 155 through 159 removed outlier: 6.104A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 41 through 43 Processing sheet with id= M, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= N, first strand: chain 'C' and resid 76 through 79 Processing sheet with id= O, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.527A pdb=" N GLY C 177 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ARG C 204 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU C 175 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 155 through 159 removed outlier: 6.105A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 41 through 43 Processing sheet with id= R, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= S, first strand: chain 'D' and resid 76 through 79 Processing sheet with id= T, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.527A pdb=" N GLY D 177 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG D 204 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU D 175 " --> pdb=" O ARG D 204 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 155 through 159 removed outlier: 6.105A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 41 through 43 Processing sheet with id= W, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= X, first strand: chain 'E' and resid 76 through 79 Processing sheet with id= Y, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.528A pdb=" N GLY E 177 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG E 204 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU E 175 " --> pdb=" O ARG E 204 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 2260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.29 Time building geometry restraints manager: 27.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15820 1.04 - 1.24: 2110 1.24 - 1.44: 5321 1.44 - 1.64: 9709 1.64 - 1.84: 170 Bond restraints: 33130 Sorted by residual: bond pdb=" NZ LYS B 303 " pdb=" HZ3 LYS B 303 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" NZ LYS D 412 " pdb=" HZ2 LYS D 412 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" NZ LYS E 45 " pdb=" HZ3 LYS E 45 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS B 5 " pdb=" HZ3 LYS B 5 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS C 5 " pdb=" HZ1 LYS C 5 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 33125 not shown) Histogram of bond angle deviations from ideal: 97.58 - 104.89: 527 104.89 - 112.19: 37269 112.19 - 119.50: 8520 119.50 - 126.80: 12913 126.80 - 134.11: 331 Bond angle restraints: 59560 Sorted by residual: angle pdb=" N ASN D 110 " pdb=" CA ASN D 110 " pdb=" CB ASN D 110 " ideal model delta sigma weight residual 110.51 117.28 -6.77 1.61e+00 3.86e-01 1.77e+01 angle pdb=" N ASN A 110 " pdb=" CA ASN A 110 " pdb=" CB ASN A 110 " ideal model delta sigma weight residual 110.51 117.28 -6.77 1.61e+00 3.86e-01 1.77e+01 angle pdb=" N ASN C 110 " pdb=" CA ASN C 110 " pdb=" CB ASN C 110 " ideal model delta sigma weight residual 110.51 117.26 -6.75 1.61e+00 3.86e-01 1.76e+01 angle pdb=" N ASN B 110 " pdb=" CA ASN B 110 " pdb=" CB ASN B 110 " ideal model delta sigma weight residual 110.51 117.26 -6.75 1.61e+00 3.86e-01 1.76e+01 angle pdb=" N ASN E 110 " pdb=" CA ASN E 110 " pdb=" CB ASN E 110 " ideal model delta sigma weight residual 110.51 117.26 -6.75 1.61e+00 3.86e-01 1.76e+01 ... (remaining 59555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.04: 15705 25.04 - 50.08: 635 50.08 - 75.13: 150 75.13 - 100.17: 35 100.17 - 125.21: 15 Dihedral angle restraints: 16540 sinusoidal: 9345 harmonic: 7195 Sorted by residual: dihedral pdb=" CA CYS B 189 " pdb=" C CYS B 189 " pdb=" N CYS B 190 " pdb=" CA CYS B 190 " ideal model delta harmonic sigma weight residual 180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N CYS C 190 " pdb=" CA CYS C 190 " ideal model delta harmonic sigma weight residual -180.00 -154.49 -25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA CYS A 189 " pdb=" C CYS A 189 " pdb=" N CYS A 190 " pdb=" CA CYS A 190 " ideal model delta harmonic sigma weight residual -180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 16537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2529 0.101 - 0.203: 156 0.203 - 0.304: 5 0.304 - 0.405: 0 0.405 - 0.506: 5 Chirality restraints: 2695 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.51e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.42e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.40e+01 ... (remaining 2692 not shown) Planarity restraints: 4700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " -0.316 2.00e-02 2.50e+03 2.73e-01 9.32e+02 pdb=" C7 NAG L 2 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.031 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " 0.475 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.315 2.00e-02 2.50e+03 2.73e-01 9.32e+02 pdb=" C7 NAG F 2 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.475 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.315 2.00e-02 2.50e+03 2.73e-01 9.31e+02 pdb=" C7 NAG H 2 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.475 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.202 2.00e-02 2.50e+03 ... (remaining 4697 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1858 2.20 - 2.80: 65428 2.80 - 3.40: 91344 3.40 - 4.00: 125115 4.00 - 4.60: 187725 Nonbonded interactions: 471470 Sorted by model distance: nonbonded pdb=" OD2 ASP D 81 " pdb=" HD1 HIS D 104 " model vdw 1.604 1.850 nonbonded pdb=" OD2 ASP A 81 " pdb=" HD1 HIS A 104 " model vdw 1.604 1.850 nonbonded pdb=" OD2 ASP E 81 " pdb=" HD1 HIS E 104 " model vdw 1.604 1.850 nonbonded pdb=" OD2 ASP C 81 " pdb=" HD1 HIS C 104 " model vdw 1.604 1.850 nonbonded pdb=" OD2 ASP B 81 " pdb=" HD1 HIS B 104 " model vdw 1.604 1.850 ... (remaining 471465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478)) selection = (chain 'B' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478)) selection = (chain 'C' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478)) selection = (chain 'D' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478)) selection = (chain 'E' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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=0.50 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: 1.640 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: 0.480 Extract box with map and model: 9.280 Check model and map are aligned: 0.540 Set scattering table: 0.250 Process input model: 120.750 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.008 0.080 17270 Z= 0.507 Angle : 0.983 6.870 23510 Z= 0.533 Chirality : 0.056 0.506 2695 Planarity : 0.014 0.273 2825 Dihedral : 15.417 125.211 7155 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.56 % Allowed : 1.68 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.75 (0.16), residues: 1960 helix: -1.22 (0.15), residues: 790 sheet: -1.05 (0.21), residues: 440 loop : -0.86 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 437 HIS 0.006 0.002 HIS B 296 PHE 0.020 0.003 PHE E 186 TYR 0.017 0.004 TYR B 194 ARG 0.009 0.001 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 377 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8474 (mpt90) REVERT: B 18 GLU cc_start: 0.8062 (tt0) cc_final: 0.7857 (tt0) REVERT: B 274 PHE cc_start: 0.7351 (m-10) cc_final: 0.7067 (m-10) REVERT: C 249 LEU cc_start: 0.8504 (tp) cc_final: 0.8242 (tm) REVERT: D 160 GLN cc_start: 0.8259 (mt0) cc_final: 0.8046 (mt0) REVERT: D 186 PHE cc_start: 0.7588 (m-80) cc_final: 0.7340 (m-80) REVERT: D 238 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8739 (mtpp) REVERT: E 92 TYR cc_start: 0.8519 (m-10) cc_final: 0.8282 (m-10) REVERT: E 455 PHE cc_start: 0.7557 (t80) cc_final: 0.7146 (t80) outliers start: 10 outliers final: 1 residues processed: 387 average time/residue: 2.1109 time to fit residues: 933.4519 Evaluate side-chains 336 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 333 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain D residue 238 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN B 160 GLN B 293 GLN C 47 GLN C 293 GLN D 26 GLN D 47 GLN E 26 GLN E 47 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17270 Z= 0.208 Angle : 0.621 5.749 23510 Z= 0.321 Chirality : 0.042 0.160 2695 Planarity : 0.004 0.061 2825 Dihedral : 12.214 120.027 3387 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.79 % Allowed : 8.72 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.08 (0.18), residues: 1960 helix: 0.86 (0.16), residues: 810 sheet: -0.51 (0.22), residues: 440 loop : -0.32 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 437 HIS 0.003 0.001 HIS B 104 PHE 0.021 0.002 PHE A 99 TYR 0.011 0.002 TYR A 117 ARG 0.008 0.001 ARG E 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 357 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7514 (mp) REVERT: A 417 VAL cc_start: 0.7488 (t) cc_final: 0.7280 (t) REVERT: B 216 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7451 (mp) REVERT: B 298 ASP cc_start: 0.7856 (t0) cc_final: 0.7573 (t0) REVERT: B 450 MET cc_start: 0.5947 (mmm) cc_final: 0.5594 (mmm) REVERT: C 18 GLU cc_start: 0.8079 (tt0) cc_final: 0.7736 (tt0) REVERT: C 472 GLU cc_start: 0.7420 (tt0) cc_final: 0.7110 (tt0) REVERT: D 186 PHE cc_start: 0.7398 (m-80) cc_final: 0.7194 (m-80) REVERT: D 446 ARG cc_start: 0.7814 (tpp80) cc_final: 0.7580 (tpp80) REVERT: E 216 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7352 (mp) REVERT: E 455 PHE cc_start: 0.7497 (t80) cc_final: 0.7128 (t80) outliers start: 32 outliers final: 17 residues processed: 374 average time/residue: 2.0285 time to fit residues: 878.4287 Evaluate side-chains 361 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 341 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 78 ARG Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A A 158 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN D 47 GLN D 158 GLN E 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17270 Z= 0.392 Angle : 0.721 11.324 23510 Z= 0.372 Chirality : 0.044 0.252 2695 Planarity : 0.006 0.066 2825 Dihedral : 11.975 111.769 3383 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.85 % Allowed : 8.44 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 1960 helix: 0.83 (0.16), residues: 855 sheet: -0.50 (0.22), residues: 435 loop : -0.19 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 148 HIS 0.004 0.001 HIS B 62 PHE 0.017 0.003 PHE B 99 TYR 0.018 0.003 TYR A 419 ARG 0.006 0.001 ARG B 4 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 332 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.6732 (t0) cc_final: 0.6369 (m110) REVERT: A 78 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8498 (mpt90) REVERT: A 174 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.7106 (t0) REVERT: A 216 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7726 (mp) REVERT: A 278 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.6015 (mpt) REVERT: B 41 ASP cc_start: 0.7702 (t0) cc_final: 0.7388 (t0) REVERT: B 450 MET cc_start: 0.5992 (mmm) cc_final: 0.5611 (mmm) REVERT: B 472 GLU cc_start: 0.7498 (tt0) cc_final: 0.7131 (tt0) REVERT: C 450 MET cc_start: 0.7002 (ptm) cc_final: 0.6734 (ptm) REVERT: C 472 GLU cc_start: 0.7566 (tt0) cc_final: 0.7123 (tt0) REVERT: D 78 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8690 (pmm150) REVERT: D 216 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7731 (mp) REVERT: D 446 ARG cc_start: 0.7865 (tpp80) cc_final: 0.7628 (tpp80) REVERT: E 92 TYR cc_start: 0.8542 (m-10) cc_final: 0.8252 (m-10) REVERT: E 216 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7533 (mp) REVERT: E 252 PHE cc_start: 0.8302 (t80) cc_final: 0.8096 (t80) REVERT: E 278 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.5551 (mpt) REVERT: E 455 PHE cc_start: 0.7567 (t80) cc_final: 0.7169 (t80) outliers start: 48 outliers final: 22 residues processed: 350 average time/residue: 1.9723 time to fit residues: 796.3246 Evaluate side-chains 358 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 328 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 GLN D 47 GLN D 106 ASN E 26 GLN E 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17270 Z= 0.249 Angle : 0.597 7.973 23510 Z= 0.308 Chirality : 0.040 0.140 2695 Planarity : 0.005 0.050 2825 Dihedral : 11.056 106.013 3383 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.63 % Allowed : 9.72 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.60 (0.18), residues: 1960 helix: 1.40 (0.17), residues: 825 sheet: -0.48 (0.23), residues: 430 loop : -0.08 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 133 HIS 0.002 0.001 HIS B 297 PHE 0.015 0.002 PHE C 470 TYR 0.011 0.002 TYR A 419 ARG 0.006 0.001 ARG E 446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 333 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.6615 (t0) cc_final: 0.6186 (m-40) REVERT: A 78 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8449 (mpt90) REVERT: A 278 MET cc_start: 0.6541 (OUTLIER) cc_final: 0.6043 (mpt) REVERT: A 417 VAL cc_start: 0.7478 (t) cc_final: 0.7268 (t) REVERT: B 41 ASP cc_start: 0.7642 (t0) cc_final: 0.7269 (t0) REVERT: B 44 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.5742 (mm-30) REVERT: B 278 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.5650 (mpt) REVERT: B 450 MET cc_start: 0.5946 (mmm) cc_final: 0.5565 (mmm) REVERT: B 472 GLU cc_start: 0.7463 (tt0) cc_final: 0.7092 (tt0) REVERT: C 294 TYR cc_start: 0.8662 (m-80) cc_final: 0.8388 (m-80) REVERT: C 472 GLU cc_start: 0.7468 (tt0) cc_final: 0.7070 (tt0) REVERT: D 78 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8722 (pmm150) REVERT: D 274 PHE cc_start: 0.6994 (m-10) cc_final: 0.6004 (m-10) REVERT: D 278 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.5580 (mpt) REVERT: D 294 TYR cc_start: 0.8637 (m-80) cc_final: 0.8309 (m-80) REVERT: D 446 ARG cc_start: 0.7838 (tpp80) cc_final: 0.7589 (tpp80) REVERT: E 216 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7502 (mp) REVERT: E 278 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.5487 (mpt) REVERT: E 455 PHE cc_start: 0.7536 (t80) cc_final: 0.7124 (t80) outliers start: 42 outliers final: 21 residues processed: 351 average time/residue: 2.0431 time to fit residues: 823.7690 Evaluate side-chains 358 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 329 time to evaluate : 5.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 47 GLN C 47 GLN D 47 GLN E 26 GLN E 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17270 Z= 0.261 Angle : 0.593 5.624 23510 Z= 0.306 Chirality : 0.040 0.164 2695 Planarity : 0.005 0.055 2825 Dihedral : 10.609 97.211 3383 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.46 % Allowed : 10.28 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.78 (0.18), residues: 1960 helix: 1.57 (0.17), residues: 830 sheet: -0.41 (0.23), residues: 430 loop : 0.02 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 133 HIS 0.002 0.001 HIS B 62 PHE 0.015 0.002 PHE C 470 TYR 0.012 0.002 TYR A 419 ARG 0.007 0.001 ARG E 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 340 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.6736 (t0) cc_final: 0.6279 (m-40) REVERT: A 78 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8157 (mpt-90) REVERT: A 278 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.6087 (mpt) REVERT: A 417 VAL cc_start: 0.7440 (t) cc_final: 0.7222 (t) REVERT: B 41 ASP cc_start: 0.7686 (t0) cc_final: 0.7347 (t0) REVERT: B 44 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.5689 (mm-30) REVERT: B 278 MET cc_start: 0.6483 (OUTLIER) cc_final: 0.5594 (mpt) REVERT: B 294 TYR cc_start: 0.8622 (m-80) cc_final: 0.8365 (m-80) REVERT: B 450 MET cc_start: 0.5958 (mmm) cc_final: 0.5555 (mmm) REVERT: B 472 GLU cc_start: 0.7477 (tt0) cc_final: 0.7130 (tt0) REVERT: C 128 TYR cc_start: 0.7332 (t80) cc_final: 0.7029 (t80) REVERT: C 294 TYR cc_start: 0.8664 (m-80) cc_final: 0.8412 (m-80) REVERT: C 472 GLU cc_start: 0.7457 (tt0) cc_final: 0.7047 (tt0) REVERT: D 78 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8557 (pmm150) REVERT: D 274 PHE cc_start: 0.6997 (m-10) cc_final: 0.5971 (m-10) REVERT: D 278 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.5496 (mpt) REVERT: D 294 TYR cc_start: 0.8618 (m-80) cc_final: 0.8318 (m-80) REVERT: D 446 ARG cc_start: 0.7839 (tpp80) cc_final: 0.7595 (tpp80) REVERT: E 216 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7543 (mp) REVERT: E 278 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.5544 (mpt) REVERT: E 455 PHE cc_start: 0.7539 (t80) cc_final: 0.7173 (t80) REVERT: E 472 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7232 (tt0) outliers start: 39 outliers final: 23 residues processed: 358 average time/residue: 1.9996 time to fit residues: 822.8000 Evaluate side-chains 361 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 329 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Chi-restraints excluded: chain E residue 472 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN D 26 GLN D 47 GLN E 26 GLN E 47 GLN E 56 GLN A ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17270 Z= 0.326 Angle : 0.636 6.015 23510 Z= 0.330 Chirality : 0.042 0.239 2695 Planarity : 0.005 0.059 2825 Dihedral : 10.539 87.895 3383 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.74 % Allowed : 9.94 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.72 (0.18), residues: 1960 helix: 1.52 (0.17), residues: 825 sheet: -0.39 (0.23), residues: 435 loop : -0.05 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 133 HIS 0.003 0.001 HIS B 297 PHE 0.016 0.002 PHE C 470 TYR 0.014 0.002 TYR A 31 ARG 0.008 0.001 ARG C 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 328 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.6805 (t0) cc_final: 0.6371 (m-40) REVERT: A 69 SER cc_start: 0.7365 (m) cc_final: 0.7072 (t) REVERT: A 78 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8172 (mpt-90) REVERT: A 216 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7819 (mp) REVERT: A 417 VAL cc_start: 0.7490 (t) cc_final: 0.7249 (t) REVERT: B 41 ASP cc_start: 0.7675 (t0) cc_final: 0.7339 (t0) REVERT: B 216 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7672 (mp) REVERT: B 294 TYR cc_start: 0.8637 (m-80) cc_final: 0.8306 (m-80) REVERT: B 450 MET cc_start: 0.5986 (mmm) cc_final: 0.5557 (mmm) REVERT: B 472 GLU cc_start: 0.7494 (tt0) cc_final: 0.7097 (tt0) REVERT: C 128 TYR cc_start: 0.7361 (t80) cc_final: 0.7046 (t80) REVERT: C 294 TYR cc_start: 0.8700 (m-80) cc_final: 0.8366 (m-80) REVERT: C 472 GLU cc_start: 0.7520 (tt0) cc_final: 0.7082 (tt0) REVERT: D 294 TYR cc_start: 0.8651 (m-80) cc_final: 0.8307 (m-80) REVERT: D 446 ARG cc_start: 0.7855 (tpp80) cc_final: 0.7616 (tpp80) REVERT: E 92 TYR cc_start: 0.8493 (m-10) cc_final: 0.8271 (m-10) REVERT: E 181 LYS cc_start: 0.7934 (tttt) cc_final: 0.7643 (tmtt) REVERT: E 216 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7622 (mp) REVERT: E 278 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.5515 (mpt) REVERT: E 455 PHE cc_start: 0.7557 (t80) cc_final: 0.7180 (t80) REVERT: E 472 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7254 (tt0) outliers start: 44 outliers final: 24 residues processed: 343 average time/residue: 1.9777 time to fit residues: 782.5115 Evaluate side-chains 360 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 330 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 416 GLU Chi-restraints excluded: chain E residue 472 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 107 optimal weight: 0.0370 chunk 137 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 158 optimal weight: 0.0040 chunk 105 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 overall best weight: 0.4870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 427 GLN C 47 GLN D 47 GLN E 26 GLN E 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17270 Z= 0.156 Angle : 0.523 5.619 23510 Z= 0.269 Chirality : 0.040 0.290 2695 Planarity : 0.004 0.055 2825 Dihedral : 9.947 79.528 3383 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.73 % Allowed : 11.17 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.23 (0.19), residues: 1960 helix: 1.92 (0.17), residues: 830 sheet: -0.14 (0.23), residues: 430 loop : 0.25 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 133 HIS 0.002 0.000 HIS B 104 PHE 0.012 0.001 PHE E 470 TYR 0.007 0.001 TYR D 194 ARG 0.009 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 335 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.6749 (t0) cc_final: 0.6369 (m-40) REVERT: A 69 SER cc_start: 0.7328 (m) cc_final: 0.7039 (t) REVERT: A 78 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8227 (mpt-90) REVERT: A 212 LEU cc_start: 0.8056 (mt) cc_final: 0.7610 (mm) REVERT: B 70 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6988 (mt-10) REVERT: B 450 MET cc_start: 0.5898 (mmm) cc_final: 0.5460 (mmm) REVERT: C 294 TYR cc_start: 0.8672 (m-80) cc_final: 0.8462 (m-80) REVERT: C 455 PHE cc_start: 0.7472 (t80) cc_final: 0.7263 (t80) REVERT: C 472 GLU cc_start: 0.7363 (tt0) cc_final: 0.7083 (tt0) REVERT: D 97 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: D 294 TYR cc_start: 0.8595 (m-80) cc_final: 0.8379 (m-80) REVERT: D 446 ARG cc_start: 0.7811 (tpp80) cc_final: 0.7580 (tpp80) REVERT: E 216 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7525 (mm) REVERT: E 455 PHE cc_start: 0.7492 (t80) cc_final: 0.7148 (t80) outliers start: 26 outliers final: 15 residues processed: 345 average time/residue: 2.0514 time to fit residues: 813.6900 Evaluate side-chains 343 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 325 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN D 26 GLN D 47 GLN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17270 Z= 0.323 Angle : 0.624 6.118 23510 Z= 0.322 Chirality : 0.042 0.313 2695 Planarity : 0.005 0.059 2825 Dihedral : 10.034 72.075 3383 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.68 % Allowed : 11.79 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.94 (0.18), residues: 1960 helix: 1.70 (0.17), residues: 830 sheet: -0.32 (0.23), residues: 430 loop : 0.10 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 148 HIS 0.003 0.001 HIS E 297 PHE 0.015 0.002 PHE A 470 TYR 0.016 0.002 TYR A 31 ARG 0.008 0.001 ARG C 446 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 329 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6279 (mm-30) REVERT: A 78 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8222 (mpt-90) REVERT: B 41 ASP cc_start: 0.7661 (t0) cc_final: 0.7313 (t0) REVERT: B 450 MET cc_start: 0.5985 (mmm) cc_final: 0.5537 (mmm) REVERT: C 128 TYR cc_start: 0.7323 (t80) cc_final: 0.7018 (t80) REVERT: C 294 TYR cc_start: 0.8704 (m-80) cc_final: 0.8380 (m-80) REVERT: C 472 GLU cc_start: 0.7455 (tt0) cc_final: 0.7046 (tt0) REVERT: D 97 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: D 294 TYR cc_start: 0.8606 (m-80) cc_final: 0.8287 (m-80) REVERT: D 446 ARG cc_start: 0.7851 (tpp80) cc_final: 0.7618 (tpp80) REVERT: E 44 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.5673 (mm-30) REVERT: E 92 TYR cc_start: 0.8510 (m-10) cc_final: 0.8244 (m-10) REVERT: E 216 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7623 (mp) REVERT: E 455 PHE cc_start: 0.7523 (t80) cc_final: 0.7157 (t80) outliers start: 25 outliers final: 18 residues processed: 341 average time/residue: 2.0486 time to fit residues: 803.1360 Evaluate side-chains 350 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 327 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 158 optimal weight: 0.3980 chunk 165 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN D 47 GLN D 106 ASN E 26 GLN E 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17270 Z= 0.184 Angle : 0.550 9.378 23510 Z= 0.282 Chirality : 0.040 0.289 2695 Planarity : 0.004 0.058 2825 Dihedral : 9.774 71.458 3383 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.56 % Allowed : 12.12 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.13 (0.19), residues: 1960 helix: 1.88 (0.17), residues: 825 sheet: -0.17 (0.24), residues: 420 loop : 0.13 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 133 HIS 0.002 0.001 HIS B 104 PHE 0.013 0.001 PHE E 470 TYR 0.009 0.001 TYR D 273 ARG 0.009 0.001 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 337 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6262 (mm-30) REVERT: A 78 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8239 (mpt-90) REVERT: B 41 ASP cc_start: 0.7658 (t0) cc_final: 0.7274 (t0) REVERT: B 450 MET cc_start: 0.5912 (mmm) cc_final: 0.5472 (mmm) REVERT: C 128 TYR cc_start: 0.7318 (t80) cc_final: 0.7009 (t80) REVERT: C 294 TYR cc_start: 0.8672 (m-80) cc_final: 0.8453 (m-80) REVERT: C 450 MET cc_start: 0.6826 (ptt) cc_final: 0.6590 (ptt) REVERT: C 472 GLU cc_start: 0.7395 (tt0) cc_final: 0.7048 (tt0) REVERT: D 97 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: D 294 TYR cc_start: 0.8591 (m-80) cc_final: 0.8361 (m-80) REVERT: D 446 ARG cc_start: 0.7832 (tpp80) cc_final: 0.7602 (tpp80) REVERT: E 216 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7569 (mp) REVERT: E 254 LEU cc_start: 0.7568 (mt) cc_final: 0.7347 (mt) REVERT: E 455 PHE cc_start: 0.7485 (t80) cc_final: 0.7136 (t80) outliers start: 23 outliers final: 18 residues processed: 348 average time/residue: 2.0503 time to fit residues: 822.8118 Evaluate side-chains 351 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 329 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 119 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN D 26 GLN D 47 GLN E 26 GLN E 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17270 Z= 0.174 Angle : 0.533 6.603 23510 Z= 0.274 Chirality : 0.039 0.290 2695 Planarity : 0.004 0.061 2825 Dihedral : 9.220 74.661 3383 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.62 % Allowed : 12.18 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.32 (0.19), residues: 1960 helix: 2.05 (0.17), residues: 825 sheet: -0.09 (0.24), residues: 420 loop : 0.22 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 66 HIS 0.002 0.001 HIS B 104 PHE 0.012 0.001 PHE E 470 TYR 0.008 0.001 TYR D 419 ARG 0.009 0.000 ARG C 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 331 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6242 (mm-30) REVERT: A 67 ASN cc_start: 0.6205 (t0) cc_final: 0.5726 (m110) REVERT: A 78 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8263 (mpt-90) REVERT: A 436 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6769 (mm-30) REVERT: A 450 MET cc_start: 0.5769 (mmm) cc_final: 0.5061 (mmm) REVERT: B 41 ASP cc_start: 0.7665 (t0) cc_final: 0.7324 (t0) REVERT: B 44 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6258 (tm-30) REVERT: B 450 MET cc_start: 0.5913 (mmm) cc_final: 0.5469 (mmm) REVERT: C 128 TYR cc_start: 0.7308 (t80) cc_final: 0.6992 (t80) REVERT: C 294 TYR cc_start: 0.8672 (m-80) cc_final: 0.8442 (m-80) REVERT: C 322 MET cc_start: 0.7683 (mtp) cc_final: 0.7366 (mtm) REVERT: C 472 GLU cc_start: 0.7348 (tt0) cc_final: 0.7085 (tt0) REVERT: D 97 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: D 294 TYR cc_start: 0.8580 (m-80) cc_final: 0.8372 (m-80) REVERT: D 446 ARG cc_start: 0.7828 (tpp80) cc_final: 0.7609 (tpp80) REVERT: E 216 ILE cc_start: 0.7720 (mp) cc_final: 0.7514 (mm) REVERT: E 254 LEU cc_start: 0.7561 (mt) cc_final: 0.7333 (mt) REVERT: E 455 PHE cc_start: 0.7477 (t80) cc_final: 0.7139 (t80) outliers start: 24 outliers final: 18 residues processed: 342 average time/residue: 2.0462 time to fit residues: 804.4163 Evaluate side-chains 344 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 322 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 47 GLN D 47 GLN D 106 ASN E 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.152944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.133701 restraints weight = 58816.397| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.40 r_work: 0.3262 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17270 Z= 0.247 Angle : 0.583 5.796 23510 Z= 0.301 Chirality : 0.040 0.259 2695 Planarity : 0.005 0.061 2825 Dihedral : 9.317 79.667 3383 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.56 % Allowed : 12.35 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.14 (0.18), residues: 1960 helix: 1.91 (0.17), residues: 830 sheet: -0.28 (0.23), residues: 430 loop : 0.19 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 133 HIS 0.003 0.001 HIS B 297 PHE 0.014 0.002 PHE A 470 TYR 0.012 0.002 TYR A 31 ARG 0.008 0.001 ARG C 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13111.92 seconds wall clock time: 228 minutes 53.59 seconds (13733.59 seconds total)