Starting phenix.real_space_refine on Mon Mar 18 14:28:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/03_2024/6kff_9971.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/03_2024/6kff_9971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/03_2024/6kff_9971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/03_2024/6kff_9971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/03_2024/6kff_9971.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kff_9971/03_2024/6kff_9971.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 14072 2.51 5 N 3432 2.21 5 O 3592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 54": "OD1" <-> "OD2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ASP 175": "OD1" <-> "OD2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ASP 136": "OD1" <-> "OD2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B ARG 181": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ASP 175": "OD1" <-> "OD2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ASP 175": "OD1" <-> "OD2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 54": "OD1" <-> "OD2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 123": "NH1" <-> "NH2" Residue "E ASP 136": "OD1" <-> "OD2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E ASP 175": "OD1" <-> "OD2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "F TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 123": "NH1" <-> "NH2" Residue "F ASP 136": "OD1" <-> "OD2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F ARG 161": "NH1" <-> "NH2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F ASP 175": "OD1" <-> "OD2" Residue "F ARG 181": "NH1" <-> "NH2" Residue "F ARG 184": "NH1" <-> "NH2" Residue "G PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 54": "OD1" <-> "OD2" Residue "G TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "G ASP 136": "OD1" <-> "OD2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G ARG 161": "NH1" <-> "NH2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G ASP 175": "OD1" <-> "OD2" Residue "G ARG 181": "NH1" <-> "NH2" Residue "G ARG 184": "NH1" <-> "NH2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 54": "OD1" <-> "OD2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H ASP 136": "OD1" <-> "OD2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H ARG 161": "NH1" <-> "NH2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H ASP 175": "OD1" <-> "OD2" Residue "H ARG 181": "NH1" <-> "NH2" Residue "H ARG 184": "NH1" <-> "NH2" 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: 21192 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2649 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 10.20, per 1000 atoms: 0.48 Number of scatterers: 21192 At special positions: 0 Unit cell: (121.968, 121.968, 108.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3592 8.00 N 3432 7.00 C 14072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 58 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 58 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 76 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 58 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 58 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 76 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS H 58 " - pdb=" SG CYS H 265 " distance=2.03 Simple disulfide: pdb=" SG CYS H 76 " - pdb=" SG CYS H 248 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.45 Conformation dependent library (CDL) restraints added in 3.3 seconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4960 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 8 sheets defined 71.7% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Proline residue: A 122 - end of helix removed outlier: 3.830A pdb=" N GLY A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS A 159 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 212 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 350 Processing helix chain 'A' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Proline residue: B 122 - end of helix removed outlier: 3.829A pdb=" N GLY B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 168 Processing helix chain 'B' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 212 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 305 " --> pdb=" O TYR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 350 Processing helix chain 'B' and resid 351 through 364 removed outlier: 3.537A pdb=" N LEU B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG B 362 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN B 363 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG C 33 " --> pdb=" O ARG C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Proline residue: C 122 - end of helix removed outlier: 3.829A pdb=" N GLY C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 168 Processing helix chain 'C' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 212 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 276 through 305 removed outlier: 4.070A pdb=" N PHE C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 305 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 350 Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.537A pdb=" N LEU C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN C 363 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 364 " --> pdb=" O SER C 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 53 removed outlier: 4.057A pdb=" N ARG D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 79 removed outlier: 4.759A pdb=" N GLN D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) Proline residue: D 122 - end of helix removed outlier: 3.830A pdb=" N GLY D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 152 removed outlier: 3.879A pdb=" N ALA D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 168 Processing helix chain 'D' and resid 168 through 182 removed outlier: 3.915A pdb=" N TYR D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 212 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 305 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 350 Processing helix chain 'D' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU D 357 " --> pdb=" O PRO D 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN D 363 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE D 364 " --> pdb=" O SER D 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG E 33 " --> pdb=" O ARG E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 79 removed outlier: 4.759A pdb=" N GLN E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) Proline residue: E 122 - end of helix removed outlier: 3.829A pdb=" N GLY E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 159 removed outlier: 4.146A pdb=" N LYS E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 212 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS E 305 " --> pdb=" O TYR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 309 through 316 Processing helix chain 'E' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE E 330 " --> pdb=" O SER E 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 350 Processing helix chain 'E' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU E 357 " --> pdb=" O PRO E 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG E 362 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN E 363 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE E 364 " --> pdb=" O SER E 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 134 removed outlier: 4.479A pdb=" N ALA F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) Proline residue: F 122 - end of helix removed outlier: 3.830A pdb=" N GLY F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 152 removed outlier: 3.878A pdb=" N ALA F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 168 Processing helix chain 'F' and resid 168 through 182 removed outlier: 3.917A pdb=" N TYR F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 212 Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE F 282 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS F 305 " --> pdb=" O TYR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE F 331 " --> pdb=" O ASP F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 350 Processing helix chain 'F' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU F 357 " --> pdb=" O PRO F 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG F 362 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN F 363 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE F 364 " --> pdb=" O SER F 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 53 removed outlier: 4.058A pdb=" N ARG G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 79 removed outlier: 4.758A pdb=" N GLN G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 134 removed outlier: 4.479A pdb=" N ALA G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Proline residue: G 122 - end of helix removed outlier: 3.829A pdb=" N GLY G 134 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.879A pdb=" N ALA G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 removed outlier: 4.146A pdb=" N LYS G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 168 Processing helix chain 'G' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR G 172 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS G 182 " --> pdb=" O ARG G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 212 Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'G' and resid 276 through 305 removed outlier: 4.070A pdb=" N PHE G 282 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS G 305 " --> pdb=" O TYR G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 308 No H-bonds generated for 'chain 'G' and resid 306 through 308' Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 326 through 335 removed outlier: 3.548A pdb=" N PHE G 330 " --> pdb=" O SER G 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE G 331 " --> pdb=" O ASP G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 350 Processing helix chain 'G' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU G 357 " --> pdb=" O PRO G 353 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG G 362 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN G 363 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE G 364 " --> pdb=" O SER G 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 53 removed outlier: 4.057A pdb=" N ARG H 33 " --> pdb=" O ARG H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 79 removed outlier: 4.759A pdb=" N GLN H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 134 removed outlier: 4.480A pdb=" N ALA H 113 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Proline residue: H 122 - end of helix removed outlier: 3.829A pdb=" N GLY H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 152 removed outlier: 3.879A pdb=" N ALA H 140 " --> pdb=" O ASP H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 159 removed outlier: 4.147A pdb=" N LYS H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 168 Processing helix chain 'H' and resid 168 through 182 removed outlier: 3.916A pdb=" N TYR H 172 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS H 182 " --> pdb=" O ARG H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 212 Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'H' and resid 276 through 305 removed outlier: 4.071A pdb=" N PHE H 282 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS H 305 " --> pdb=" O TYR H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 308 No H-bonds generated for 'chain 'H' and resid 306 through 308' Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 326 through 335 removed outlier: 3.549A pdb=" N PHE H 330 " --> pdb=" O SER H 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE H 331 " --> pdb=" O ASP H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 350 Processing helix chain 'H' and resid 351 through 364 removed outlier: 3.536A pdb=" N LEU H 357 " --> pdb=" O PRO H 353 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG H 362 " --> pdb=" O THR H 358 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN H 363 " --> pdb=" O ILE H 359 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE H 364 " --> pdb=" O SER H 360 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 57 Processing sheet with id=AA4, first strand: chain 'D' and resid 56 through 57 Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 57 Processing sheet with id=AA6, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AA7, first strand: chain 'G' and resid 56 through 57 Processing sheet with id=AA8, first strand: chain 'H' and resid 56 through 57 1240 hydrogen bonds defined for protein. 3624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.09 Time building geometry restraints manager: 8.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6312 1.34 - 1.46: 5601 1.46 - 1.58: 9791 1.58 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 21832 Sorted by residual: bond pdb=" C ARG G 168 " pdb=" N PRO G 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.17e-01 bond pdb=" C ARG H 168 " pdb=" N PRO H 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.07e-01 bond pdb=" C ARG D 168 " pdb=" N PRO D 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.06e-01 bond pdb=" C ARG E 168 " pdb=" N PRO E 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.74e-01 bond pdb=" C ARG A 168 " pdb=" N PRO A 169 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.66e-01 ... (remaining 21827 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.08: 534 107.08 - 113.82: 11986 113.82 - 120.56: 9341 120.56 - 127.30: 7556 127.30 - 134.04: 327 Bond angle restraints: 29744 Sorted by residual: angle pdb=" C TRP G 107 " pdb=" N VAL G 108 " pdb=" CA VAL G 108 " ideal model delta sigma weight residual 120.33 122.46 -2.13 8.00e-01 1.56e+00 7.06e+00 angle pdb=" C TRP B 107 " pdb=" N VAL B 108 " pdb=" CA VAL B 108 " ideal model delta sigma weight residual 120.33 122.45 -2.12 8.00e-01 1.56e+00 7.00e+00 angle pdb=" C TRP C 107 " pdb=" N VAL C 108 " pdb=" CA VAL C 108 " ideal model delta sigma weight residual 120.33 122.45 -2.12 8.00e-01 1.56e+00 6.99e+00 angle pdb=" C TRP F 107 " pdb=" N VAL F 108 " pdb=" CA VAL F 108 " ideal model delta sigma weight residual 120.33 122.45 -2.12 8.00e-01 1.56e+00 6.99e+00 angle pdb=" C TRP E 107 " pdb=" N VAL E 108 " pdb=" CA VAL E 108 " ideal model delta sigma weight residual 120.33 122.44 -2.11 8.00e-01 1.56e+00 6.93e+00 ... (remaining 29739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 10949 17.32 - 34.64: 1251 34.64 - 51.96: 224 51.96 - 69.28: 16 69.28 - 86.60: 40 Dihedral angle restraints: 12480 sinusoidal: 4840 harmonic: 7640 Sorted by residual: dihedral pdb=" CB CYS F 76 " pdb=" SG CYS F 76 " pdb=" SG CYS F 248 " pdb=" CB CYS F 248 " ideal model delta sinusoidal sigma weight residual 93.00 137.02 -44.02 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS G 76 " pdb=" SG CYS G 76 " pdb=" SG CYS G 248 " pdb=" CB CYS G 248 " ideal model delta sinusoidal sigma weight residual 93.00 137.01 -44.01 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS A 76 " pdb=" SG CYS A 76 " pdb=" SG CYS A 248 " pdb=" CB CYS A 248 " ideal model delta sinusoidal sigma weight residual 93.00 137.00 -44.00 1 1.00e+01 1.00e-02 2.69e+01 ... (remaining 12477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1859 0.026 - 0.051: 855 0.051 - 0.077: 412 0.077 - 0.103: 108 0.103 - 0.129: 54 Chirality restraints: 3288 Sorted by residual: chirality pdb=" CA TRP B 236 " pdb=" N TRP B 236 " pdb=" C TRP B 236 " pdb=" CB TRP B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA TRP G 236 " pdb=" N TRP G 236 " pdb=" C TRP G 236 " pdb=" CB TRP G 236 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA TRP F 236 " pdb=" N TRP F 236 " pdb=" C TRP F 236 " pdb=" CB TRP F 236 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 3285 not shown) Planarity restraints: 3632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 119 " -0.010 2.00e-02 2.50e+03 9.91e-03 1.72e+00 pdb=" CG PHE D 119 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE D 119 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 119 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE D 119 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 119 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 119 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 119 " -0.010 2.00e-02 2.50e+03 9.75e-03 1.66e+00 pdb=" CG PHE F 119 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE F 119 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE F 119 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 119 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 119 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 119 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 119 " -0.009 2.00e-02 2.50e+03 9.75e-03 1.66e+00 pdb=" CG PHE C 119 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE C 119 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 119 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 119 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 119 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 119 " -0.002 2.00e-02 2.50e+03 ... (remaining 3629 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1164 2.73 - 3.27: 22887 3.27 - 3.81: 35035 3.81 - 4.36: 38025 4.36 - 4.90: 66422 Nonbonded interactions: 163533 Sorted by model distance: nonbonded pdb=" O ASN D 31 " pdb=" OG1 THR D 35 " model vdw 2.182 2.440 nonbonded pdb=" O ASN A 31 " pdb=" OG1 THR A 35 " model vdw 2.183 2.440 nonbonded pdb=" O ASN B 31 " pdb=" OG1 THR B 35 " model vdw 2.183 2.440 nonbonded pdb=" O ASN G 31 " pdb=" OG1 THR G 35 " model vdw 2.183 2.440 nonbonded pdb=" O ASN F 31 " pdb=" OG1 THR F 35 " model vdw 2.183 2.440 ... (remaining 163528 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 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: 0.010 Extract box with map and model: 2.540 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 51.610 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.004 0.026 21832 Z= 0.230 Angle : 0.604 7.440 29744 Z= 0.321 Chirality : 0.038 0.129 3288 Planarity : 0.003 0.021 3632 Dihedral : 15.084 86.599 7472 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 0.35 % Allowed : 6.96 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 2496 helix: -0.50 (0.11), residues: 1672 sheet: -4.64 (0.29), residues: 80 loop : -4.12 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 68 HIS 0.004 0.001 HIS A 50 PHE 0.023 0.001 PHE D 119 TYR 0.009 0.001 TYR B 110 ARG 0.002 0.000 ARG H 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 926 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LEU cc_start: 0.9301 (tt) cc_final: 0.9094 (tt) REVERT: A 153 ASP cc_start: 0.8634 (m-30) cc_final: 0.8271 (m-30) REVERT: A 166 GLU cc_start: 0.7628 (pt0) cc_final: 0.7270 (pt0) REVERT: A 175 ASP cc_start: 0.8000 (m-30) cc_final: 0.7429 (m-30) REVERT: A 194 LEU cc_start: 0.9418 (mt) cc_final: 0.9043 (mt) REVERT: A 208 TYR cc_start: 0.8326 (t80) cc_final: 0.7846 (t80) REVERT: A 304 ASN cc_start: 0.8695 (t0) cc_final: 0.8389 (t0) REVERT: A 310 LYS cc_start: 0.6931 (ttpt) cc_final: 0.6552 (tptt) REVERT: A 339 LEU cc_start: 0.9254 (tp) cc_final: 0.9036 (tp) REVERT: A 353 PRO cc_start: 0.9486 (Cg_endo) cc_final: 0.9219 (Cg_exo) REVERT: B 58 CYS cc_start: 0.6717 (m) cc_final: 0.6494 (m) REVERT: B 146 ARG cc_start: 0.8918 (ttp80) cc_final: 0.8343 (mtm110) REVERT: B 153 ASP cc_start: 0.8678 (m-30) cc_final: 0.8243 (m-30) REVERT: B 172 TYR cc_start: 0.9068 (t80) cc_final: 0.8817 (t80) REVERT: B 270 ASN cc_start: 0.9167 (t0) cc_final: 0.8855 (t0) REVERT: B 304 ASN cc_start: 0.8321 (t0) cc_final: 0.7817 (t0) REVERT: B 310 LYS cc_start: 0.7220 (ttpt) cc_final: 0.6514 (tptt) REVERT: B 332 SER cc_start: 0.9205 (t) cc_final: 0.8999 (t) REVERT: B 353 PRO cc_start: 0.9576 (Cg_endo) cc_final: 0.9325 (Cg_exo) REVERT: B 359 ILE cc_start: 0.9395 (tp) cc_final: 0.9132 (tp) REVERT: C 154 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8066 (mtmt) REVERT: C 157 LYS cc_start: 0.8268 (tptt) cc_final: 0.7688 (ttpp) REVERT: C 198 TRP cc_start: 0.8737 (t-100) cc_final: 0.8528 (t-100) REVERT: C 208 TYR cc_start: 0.8275 (t80) cc_final: 0.7811 (t80) REVERT: C 310 LYS cc_start: 0.6681 (ttpt) cc_final: 0.6165 (tptt) REVERT: C 339 LEU cc_start: 0.9253 (tp) cc_final: 0.9039 (tp) REVERT: C 353 PRO cc_start: 0.9551 (Cg_endo) cc_final: 0.9235 (Cg_exo) REVERT: C 359 ILE cc_start: 0.9411 (tp) cc_final: 0.9207 (tp) REVERT: D 58 CYS cc_start: 0.7177 (m) cc_final: 0.6803 (m) REVERT: D 146 ARG cc_start: 0.8910 (ttp80) cc_final: 0.8286 (mtp-110) REVERT: D 192 TYR cc_start: 0.9016 (t80) cc_final: 0.8656 (t80) REVERT: D 270 ASN cc_start: 0.9148 (t0) cc_final: 0.8821 (t0) REVERT: D 304 ASN cc_start: 0.8353 (t0) cc_final: 0.8030 (t0) REVERT: D 310 LYS cc_start: 0.6960 (ttpt) cc_final: 0.6510 (tptt) REVERT: D 325 ILE cc_start: 0.8840 (mp) cc_final: 0.8622 (mp) REVERT: D 353 PRO cc_start: 0.9527 (Cg_endo) cc_final: 0.9307 (Cg_exo) REVERT: D 359 ILE cc_start: 0.9389 (tp) cc_final: 0.9184 (tp) REVERT: E 65 ASN cc_start: 0.7162 (p0) cc_final: 0.6726 (p0) REVERT: E 68 TRP cc_start: 0.7866 (t-100) cc_final: 0.7656 (t-100) REVERT: E 157 LYS cc_start: 0.8300 (tptt) cc_final: 0.7881 (ttpp) REVERT: E 166 GLU cc_start: 0.7558 (pt0) cc_final: 0.7223 (pt0) REVERT: E 178 ARG cc_start: 0.8938 (ttm-80) cc_final: 0.8667 (ttp-110) REVERT: E 208 TYR cc_start: 0.8103 (t80) cc_final: 0.7539 (t80) REVERT: E 310 LYS cc_start: 0.7104 (ttpt) cc_final: 0.6594 (tptt) REVERT: E 339 LEU cc_start: 0.9204 (tp) cc_final: 0.9002 (tp) REVERT: F 58 CYS cc_start: 0.7240 (m) cc_final: 0.6896 (m) REVERT: F 157 LYS cc_start: 0.8360 (tptt) cc_final: 0.7717 (ttmm) REVERT: F 194 LEU cc_start: 0.9221 (mt) cc_final: 0.8908 (mt) REVERT: F 310 LYS cc_start: 0.7153 (ttpt) cc_final: 0.6762 (tptt) REVERT: F 353 PRO cc_start: 0.9581 (Cg_endo) cc_final: 0.9301 (Cg_exo) REVERT: G 154 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8243 (mtpt) REVERT: G 157 LYS cc_start: 0.8301 (tptt) cc_final: 0.7725 (ttpp) REVERT: G 208 TYR cc_start: 0.8240 (t80) cc_final: 0.7752 (t80) REVERT: G 310 LYS cc_start: 0.6964 (ttpt) cc_final: 0.6236 (tptt) REVERT: G 322 LYS cc_start: 0.7669 (pttm) cc_final: 0.6898 (mptt) REVERT: G 339 LEU cc_start: 0.9308 (tp) cc_final: 0.9078 (tp) REVERT: G 353 PRO cc_start: 0.9542 (Cg_endo) cc_final: 0.9273 (Cg_exo) REVERT: G 359 ILE cc_start: 0.9350 (tp) cc_final: 0.9144 (tp) REVERT: H 58 CYS cc_start: 0.7131 (m) cc_final: 0.6644 (m) REVERT: H 192 TYR cc_start: 0.8960 (t80) cc_final: 0.8760 (t80) REVERT: H 310 LYS cc_start: 0.7196 (ttpt) cc_final: 0.6603 (tptt) REVERT: H 313 LYS cc_start: 0.9300 (ttmt) cc_final: 0.9082 (ttmm) outliers start: 8 outliers final: 6 residues processed: 928 average time/residue: 0.3506 time to fit residues: 480.1579 Evaluate side-chains 753 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 747 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain H residue 171 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 232 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 50 HIS A 234 ASN A 247 HIS A 329 GLN B 21 GLN B 234 ASN B 247 HIS B 329 GLN C 21 GLN C 206 GLN C 234 ASN C 247 HIS C 329 GLN D 21 GLN D 234 ASN D 247 HIS D 329 GLN E 21 GLN E 50 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN E 247 HIS E 329 GLN F 21 GLN F 50 HIS F 234 ASN F 247 HIS F 329 GLN G 21 GLN G 234 ASN G 247 HIS G 329 GLN H 21 GLN H 50 HIS H 234 ASN H 247 HIS H 329 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21832 Z= 0.289 Angle : 0.651 10.084 29744 Z= 0.315 Chirality : 0.042 0.177 3288 Planarity : 0.004 0.040 3632 Dihedral : 4.941 23.689 2798 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 4.52 % Allowed : 20.70 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.17), residues: 2496 helix: 0.50 (0.12), residues: 1688 sheet: -4.21 (0.36), residues: 80 loop : -3.64 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 59 HIS 0.010 0.002 HIS F 50 PHE 0.022 0.001 PHE H 124 TYR 0.017 0.001 TYR G 301 ARG 0.004 0.000 ARG E 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 775 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8321 (ttm170) cc_final: 0.8032 (ttp-170) REVERT: A 137 LEU cc_start: 0.9404 (tt) cc_final: 0.9198 (tt) REVERT: A 153 ASP cc_start: 0.8492 (m-30) cc_final: 0.8154 (m-30) REVERT: A 157 LYS cc_start: 0.8231 (tptt) cc_final: 0.7639 (ttmm) REVERT: A 208 TYR cc_start: 0.8207 (t80) cc_final: 0.7750 (t80) REVERT: A 310 LYS cc_start: 0.6945 (ttpt) cc_final: 0.6367 (tptm) REVERT: A 353 PRO cc_start: 0.9440 (Cg_endo) cc_final: 0.9189 (Cg_exo) REVERT: B 146 ARG cc_start: 0.8913 (ttp80) cc_final: 0.8321 (mtm110) REVERT: B 153 ASP cc_start: 0.8723 (m-30) cc_final: 0.8340 (m-30) REVERT: B 158 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.8018 (t80) REVERT: B 161 ARG cc_start: 0.8199 (ttp-110) cc_final: 0.7896 (ttp-110) REVERT: B 192 TYR cc_start: 0.8980 (t80) cc_final: 0.8708 (t80) REVERT: B 208 TYR cc_start: 0.8354 (t80) cc_final: 0.8093 (t80) REVERT: B 310 LYS cc_start: 0.7155 (ttpt) cc_final: 0.6545 (tptt) REVERT: B 332 SER cc_start: 0.9044 (t) cc_final: 0.8828 (t) REVERT: B 359 ILE cc_start: 0.9445 (tp) cc_final: 0.9114 (tp) REVERT: C 59 TRP cc_start: 0.8154 (t-100) cc_final: 0.7942 (t60) REVERT: C 64 PHE cc_start: 0.8280 (m-80) cc_final: 0.7881 (m-10) REVERT: C 65 ASN cc_start: 0.7317 (p0) cc_final: 0.6835 (p0) REVERT: C 154 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8206 (mtpt) REVERT: C 157 LYS cc_start: 0.8230 (tptt) cc_final: 0.7781 (ttpp) REVERT: C 198 TRP cc_start: 0.8778 (t-100) cc_final: 0.8528 (t-100) REVERT: C 208 TYR cc_start: 0.8231 (t80) cc_final: 0.7788 (t80) REVERT: C 310 LYS cc_start: 0.6762 (ttpt) cc_final: 0.6159 (tptt) REVERT: C 359 ILE cc_start: 0.9392 (tp) cc_final: 0.9154 (tp) REVERT: D 146 ARG cc_start: 0.8903 (ttp80) cc_final: 0.8317 (mtm110) REVERT: D 192 TYR cc_start: 0.9022 (t80) cc_final: 0.8702 (t80) REVERT: D 267 LEU cc_start: 0.9290 (mp) cc_final: 0.9055 (mt) REVERT: D 310 LYS cc_start: 0.7156 (ttpt) cc_final: 0.6747 (tptt) REVERT: D 332 SER cc_start: 0.9051 (m) cc_final: 0.8795 (t) REVERT: E 157 LYS cc_start: 0.8371 (tptt) cc_final: 0.7920 (ttmm) REVERT: E 206 GLN cc_start: 0.9273 (mm-40) cc_final: 0.8766 (mm-40) REVERT: E 208 TYR cc_start: 0.8078 (t80) cc_final: 0.7422 (t80) REVERT: E 310 LYS cc_start: 0.7226 (ttpt) cc_final: 0.6720 (tptt) REVERT: F 157 LYS cc_start: 0.8238 (tptt) cc_final: 0.7725 (ttmm) REVERT: F 244 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8367 (mtt-85) REVERT: F 310 LYS cc_start: 0.7108 (ttpt) cc_final: 0.6706 (tptt) REVERT: G 65 ASN cc_start: 0.7363 (p0) cc_final: 0.7046 (p0) REVERT: G 154 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8166 (mtpt) REVERT: G 157 LYS cc_start: 0.8268 (tptt) cc_final: 0.7769 (ttpp) REVERT: G 192 TYR cc_start: 0.8979 (t80) cc_final: 0.8674 (t80) REVERT: G 208 TYR cc_start: 0.8182 (t80) cc_final: 0.7736 (t80) REVERT: G 304 ASN cc_start: 0.8610 (t0) cc_final: 0.8374 (t0) REVERT: G 310 LYS cc_start: 0.6901 (ttpt) cc_final: 0.6297 (tptt) REVERT: G 322 LYS cc_start: 0.7776 (pttm) cc_final: 0.6739 (mptt) REVERT: H 137 LEU cc_start: 0.9336 (tt) cc_final: 0.9120 (tt) REVERT: H 192 TYR cc_start: 0.9126 (t80) cc_final: 0.8852 (t80) REVERT: H 310 LYS cc_start: 0.7121 (ttpt) cc_final: 0.6587 (tptt) REVERT: H 313 LYS cc_start: 0.9301 (ttmt) cc_final: 0.9049 (ttmm) outliers start: 102 outliers final: 77 residues processed: 818 average time/residue: 0.3336 time to fit residues: 407.5811 Evaluate side-chains 799 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 720 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 187 ASN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 187 ASN Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 187 ASN Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 332 SER Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 206 GLN B 50 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 67 GLN D 21 GLN D 50 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN F 329 GLN G 21 GLN G 50 HIS G 270 ASN H 21 GLN H 115 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21832 Z= 0.242 Angle : 0.608 8.038 29744 Z= 0.297 Chirality : 0.040 0.143 3288 Planarity : 0.003 0.028 3632 Dihedral : 4.760 22.871 2792 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.92 % Allowed : 23.45 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.17), residues: 2496 helix: 0.79 (0.13), residues: 1688 sheet: -3.91 (0.40), residues: 80 loop : -3.42 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP G 59 HIS 0.012 0.002 HIS B 50 PHE 0.014 0.001 PHE E 64 TYR 0.015 0.001 TYR F 301 ARG 0.004 0.000 ARG E 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 753 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8335 (ttm170) cc_final: 0.8030 (ttp-170) REVERT: A 137 LEU cc_start: 0.9372 (tt) cc_final: 0.9161 (tt) REVERT: A 153 ASP cc_start: 0.8469 (m-30) cc_final: 0.7799 (m-30) REVERT: A 157 LYS cc_start: 0.8210 (tptt) cc_final: 0.7564 (ttmm) REVERT: A 208 TYR cc_start: 0.8216 (t80) cc_final: 0.7535 (t80) REVERT: A 305 LYS cc_start: 0.8470 (tttm) cc_final: 0.8151 (tmtt) REVERT: A 310 LYS cc_start: 0.6986 (ttpt) cc_final: 0.6439 (tptm) REVERT: A 353 PRO cc_start: 0.9432 (Cg_endo) cc_final: 0.9204 (Cg_exo) REVERT: B 105 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.6651 (m-10) REVERT: B 146 ARG cc_start: 0.8902 (ttp80) cc_final: 0.8332 (mtm110) REVERT: B 153 ASP cc_start: 0.8740 (m-30) cc_final: 0.8323 (m-30) REVERT: B 158 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7886 (t80) REVERT: B 161 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7926 (ttp-110) REVERT: B 192 TYR cc_start: 0.8940 (t80) cc_final: 0.8693 (t80) REVERT: B 208 TYR cc_start: 0.8369 (t80) cc_final: 0.8029 (t80) REVERT: B 310 LYS cc_start: 0.7199 (ttpt) cc_final: 0.6453 (tptt) REVERT: B 332 SER cc_start: 0.8978 (t) cc_final: 0.8769 (t) REVERT: B 359 ILE cc_start: 0.9492 (tp) cc_final: 0.9191 (tp) REVERT: C 64 PHE cc_start: 0.8253 (m-80) cc_final: 0.7839 (m-10) REVERT: C 154 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8143 (mtpt) REVERT: C 157 LYS cc_start: 0.8314 (tptt) cc_final: 0.7785 (ttpp) REVERT: C 158 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7910 (t80) REVERT: C 198 TRP cc_start: 0.8793 (t-100) cc_final: 0.8551 (t-100) REVERT: C 208 TYR cc_start: 0.8198 (t80) cc_final: 0.7459 (t80) REVERT: C 305 LYS cc_start: 0.8383 (tttm) cc_final: 0.8053 (tmtt) REVERT: C 310 LYS cc_start: 0.6731 (ttpt) cc_final: 0.6042 (tptm) REVERT: C 322 LYS cc_start: 0.7636 (pttm) cc_final: 0.6659 (mptt) REVERT: C 359 ILE cc_start: 0.9394 (tp) cc_final: 0.9169 (tp) REVERT: D 65 ASN cc_start: 0.7413 (p0) cc_final: 0.7198 (p0) REVERT: D 105 TYR cc_start: 0.7302 (OUTLIER) cc_final: 0.6743 (m-10) REVERT: D 146 ARG cc_start: 0.8893 (ttp80) cc_final: 0.8321 (mtm110) REVERT: D 158 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7625 (t80) REVERT: D 192 TYR cc_start: 0.8978 (t80) cc_final: 0.8664 (t80) REVERT: D 310 LYS cc_start: 0.7117 (ttpt) cc_final: 0.6750 (tptt) REVERT: D 332 SER cc_start: 0.9078 (m) cc_final: 0.8816 (t) REVERT: E 28 ASP cc_start: 0.6770 (m-30) cc_final: 0.6530 (m-30) REVERT: E 65 ASN cc_start: 0.7100 (p0) cc_final: 0.6649 (p0) REVERT: E 157 LYS cc_start: 0.8408 (tptt) cc_final: 0.7855 (ttpp) REVERT: E 206 GLN cc_start: 0.9261 (mm-40) cc_final: 0.8640 (mm-40) REVERT: E 208 TYR cc_start: 0.8064 (t80) cc_final: 0.7613 (t80) REVERT: E 310 LYS cc_start: 0.7184 (ttpt) cc_final: 0.6698 (tptt) REVERT: F 153 ASP cc_start: 0.8720 (m-30) cc_final: 0.8234 (m-30) REVERT: F 157 LYS cc_start: 0.8284 (tptt) cc_final: 0.7882 (ttmm) REVERT: F 158 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7840 (t80) REVERT: F 244 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8240 (mtt-85) REVERT: F 304 ASN cc_start: 0.8625 (t0) cc_final: 0.8071 (t0) REVERT: F 310 LYS cc_start: 0.7237 (ttpt) cc_final: 0.6834 (tptt) REVERT: G 65 ASN cc_start: 0.6956 (p0) cc_final: 0.6516 (p0) REVERT: G 67 GLN cc_start: 0.8417 (mp10) cc_final: 0.7896 (mp10) REVERT: G 154 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8168 (mtpt) REVERT: G 157 LYS cc_start: 0.8309 (tptt) cc_final: 0.7700 (ttpp) REVERT: G 158 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7855 (t80) REVERT: G 192 TYR cc_start: 0.8955 (t80) cc_final: 0.8604 (t80) REVERT: G 208 TYR cc_start: 0.8156 (t80) cc_final: 0.7476 (t80) REVERT: G 305 LYS cc_start: 0.8330 (tttm) cc_final: 0.7977 (tmtt) REVERT: G 310 LYS cc_start: 0.6779 (ttpt) cc_final: 0.6263 (tptt) REVERT: G 322 LYS cc_start: 0.7625 (pttm) cc_final: 0.6594 (mptt) REVERT: H 137 LEU cc_start: 0.9338 (tt) cc_final: 0.9119 (tt) REVERT: H 146 ARG cc_start: 0.8886 (ttp80) cc_final: 0.8306 (mtp-110) REVERT: H 157 LYS cc_start: 0.8284 (tptt) cc_final: 0.7927 (ttmm) REVERT: H 158 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7806 (t80) REVERT: H 192 TYR cc_start: 0.9141 (t80) cc_final: 0.8883 (t80) REVERT: H 310 LYS cc_start: 0.7155 (ttpt) cc_final: 0.6502 (tptt) REVERT: H 313 LYS cc_start: 0.9299 (ttmt) cc_final: 0.9063 (ttmm) outliers start: 111 outliers final: 90 residues processed: 795 average time/residue: 0.3338 time to fit residues: 396.0983 Evaluate side-chains 828 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 729 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 187 ASN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 187 ASN Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 187 ASN Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 332 SER Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 156 optimal weight: 0.4980 chunk 233 optimal weight: 0.2980 chunk 247 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 67 GLN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS C 206 GLN D 21 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN E 50 HIS E 67 GLN F 50 HIS F 206 GLN G 50 HIS G 206 GLN G 270 ASN H 21 GLN H 50 HIS H 115 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21832 Z= 0.163 Angle : 0.571 7.802 29744 Z= 0.281 Chirality : 0.039 0.147 3288 Planarity : 0.003 0.027 3632 Dihedral : 4.579 21.606 2792 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 4.79 % Allowed : 25.93 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2496 helix: 1.05 (0.13), residues: 1656 sheet: -3.74 (0.40), residues: 80 loop : -3.24 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP C 59 HIS 0.013 0.002 HIS B 50 PHE 0.018 0.001 PHE H 64 TYR 0.014 0.001 TYR F 301 ARG 0.004 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 812 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8298 (ttm170) cc_final: 0.8020 (ttp-170) REVERT: A 137 LEU cc_start: 0.9308 (tt) cc_final: 0.9105 (tt) REVERT: A 153 ASP cc_start: 0.8536 (m-30) cc_final: 0.8173 (m-30) REVERT: A 157 LYS cc_start: 0.8221 (tptt) cc_final: 0.7102 (ttmm) REVERT: A 158 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.7481 (t80) REVERT: A 208 TYR cc_start: 0.8182 (t80) cc_final: 0.7497 (t80) REVERT: A 305 LYS cc_start: 0.8495 (tttm) cc_final: 0.8228 (tmtt) REVERT: A 310 LYS cc_start: 0.7006 (ttpt) cc_final: 0.6392 (tptm) REVERT: A 353 PRO cc_start: 0.9394 (Cg_endo) cc_final: 0.9164 (Cg_exo) REVERT: B 105 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.6641 (m-10) REVERT: B 146 ARG cc_start: 0.8895 (ttp80) cc_final: 0.8312 (mtm110) REVERT: B 153 ASP cc_start: 0.8721 (m-30) cc_final: 0.8310 (m-30) REVERT: B 158 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7816 (t80) REVERT: B 161 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.7922 (ttp-110) REVERT: B 170 SER cc_start: 0.9468 (t) cc_final: 0.9264 (m) REVERT: B 192 TYR cc_start: 0.8910 (t80) cc_final: 0.8699 (t80) REVERT: B 208 TYR cc_start: 0.8277 (t80) cc_final: 0.7947 (t80) REVERT: B 310 LYS cc_start: 0.7122 (ttpt) cc_final: 0.6444 (tptt) REVERT: B 315 TYR cc_start: 0.8268 (m-10) cc_final: 0.7512 (m-10) REVERT: B 322 LYS cc_start: 0.7819 (pttm) cc_final: 0.7119 (mptt) REVERT: B 332 SER cc_start: 0.8980 (t) cc_final: 0.8773 (t) REVERT: B 359 ILE cc_start: 0.9467 (tp) cc_final: 0.9157 (tp) REVERT: C 123 ARG cc_start: 0.8399 (ttm170) cc_final: 0.8141 (ttp-170) REVERT: C 154 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8110 (mtpt) REVERT: C 157 LYS cc_start: 0.8239 (tptt) cc_final: 0.7747 (ttpp) REVERT: C 158 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7830 (t80) REVERT: C 198 TRP cc_start: 0.8804 (t-100) cc_final: 0.8509 (t-100) REVERT: C 208 TYR cc_start: 0.8253 (t80) cc_final: 0.7803 (t80) REVERT: C 267 LEU cc_start: 0.9145 (mt) cc_final: 0.8800 (mt) REVERT: C 305 LYS cc_start: 0.8367 (tttm) cc_final: 0.8097 (tmtt) REVERT: C 310 LYS cc_start: 0.6953 (ttpt) cc_final: 0.6208 (tptm) REVERT: C 322 LYS cc_start: 0.7519 (pttm) cc_final: 0.6783 (mptt) REVERT: C 359 ILE cc_start: 0.9390 (tp) cc_final: 0.9155 (tp) REVERT: D 65 ASN cc_start: 0.7322 (p0) cc_final: 0.7100 (p0) REVERT: D 105 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6891 (m-10) REVERT: D 146 ARG cc_start: 0.8888 (ttp80) cc_final: 0.8382 (mtp-110) REVERT: D 158 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7418 (t80) REVERT: D 170 SER cc_start: 0.9380 (t) cc_final: 0.9174 (m) REVERT: D 192 TYR cc_start: 0.8932 (t80) cc_final: 0.8617 (t80) REVERT: D 310 LYS cc_start: 0.7057 (ttpt) cc_final: 0.6721 (tptt) REVERT: D 322 LYS cc_start: 0.7678 (pttm) cc_final: 0.7038 (mptt) REVERT: D 332 SER cc_start: 0.9122 (m) cc_final: 0.8865 (t) REVERT: E 65 ASN cc_start: 0.6268 (p0) cc_final: 0.5842 (p0) REVERT: E 67 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: E 129 MET cc_start: 0.7408 (tpp) cc_final: 0.7051 (tpp) REVERT: E 157 LYS cc_start: 0.8407 (tptt) cc_final: 0.7854 (ttmm) REVERT: E 158 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7533 (t80) REVERT: E 206 GLN cc_start: 0.9287 (mm-40) cc_final: 0.8604 (mm-40) REVERT: E 208 TYR cc_start: 0.8086 (t80) cc_final: 0.7620 (t80) REVERT: E 310 LYS cc_start: 0.7048 (ttpt) cc_final: 0.6618 (tptt) REVERT: E 322 LYS cc_start: 0.7449 (pttm) cc_final: 0.6524 (mptt) REVERT: F 105 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.7164 (m-10) REVERT: F 157 LYS cc_start: 0.8219 (tptt) cc_final: 0.7832 (ttmm) REVERT: F 158 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7570 (t80) REVERT: F 236 TRP cc_start: 0.8607 (p-90) cc_final: 0.7985 (p-90) REVERT: F 244 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7724 (mtt-85) REVERT: F 304 ASN cc_start: 0.8586 (t0) cc_final: 0.8046 (t0) REVERT: F 310 LYS cc_start: 0.7182 (ttpt) cc_final: 0.6793 (tptt) REVERT: F 322 LYS cc_start: 0.7791 (pttm) cc_final: 0.7177 (mptt) REVERT: G 65 ASN cc_start: 0.6764 (p0) cc_final: 0.6194 (p0) REVERT: G 67 GLN cc_start: 0.8356 (mp10) cc_final: 0.7828 (mp10) REVERT: G 70 ASN cc_start: 0.8474 (t0) cc_final: 0.8153 (t0) REVERT: G 123 ARG cc_start: 0.8373 (ttm170) cc_final: 0.8117 (ttp-170) REVERT: G 154 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8193 (mtpt) REVERT: G 157 LYS cc_start: 0.8357 (tptt) cc_final: 0.7616 (ttpp) REVERT: G 208 TYR cc_start: 0.8163 (t80) cc_final: 0.7720 (t80) REVERT: G 267 LEU cc_start: 0.9126 (mt) cc_final: 0.8802 (mt) REVERT: G 305 LYS cc_start: 0.8490 (tttm) cc_final: 0.8088 (tmtt) REVERT: G 310 LYS cc_start: 0.7064 (ttpt) cc_final: 0.6385 (tptm) REVERT: G 322 LYS cc_start: 0.7464 (pttm) cc_final: 0.6737 (mptt) REVERT: H 105 TYR cc_start: 0.7454 (OUTLIER) cc_final: 0.7171 (m-10) REVERT: H 146 ARG cc_start: 0.8866 (ttp80) cc_final: 0.8365 (mtm110) REVERT: H 157 LYS cc_start: 0.8308 (tptt) cc_final: 0.7874 (ttmm) REVERT: H 158 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7483 (t80) REVERT: H 192 TYR cc_start: 0.9118 (t80) cc_final: 0.8887 (t80) REVERT: H 310 LYS cc_start: 0.7135 (ttpt) cc_final: 0.6664 (tptt) REVERT: H 313 LYS cc_start: 0.9275 (ttmt) cc_final: 0.9053 (ttmm) REVERT: H 315 TYR cc_start: 0.8315 (m-10) cc_final: 0.7598 (m-10) REVERT: H 322 LYS cc_start: 0.7793 (pttm) cc_final: 0.7130 (mptt) REVERT: H 345 MET cc_start: 0.9089 (mmt) cc_final: 0.8741 (mmp) outliers start: 108 outliers final: 74 residues processed: 865 average time/residue: 0.3204 time to fit residues: 419.0512 Evaluate side-chains 839 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 752 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 187 ASN Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 187 ASN Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 3 optimal weight: 0.0770 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 211 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 67 GLN A 206 GLN B 50 HIS ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS D 21 GLN D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS G 270 ASN H 21 GLN H 50 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21832 Z= 0.220 Angle : 0.583 11.636 29744 Z= 0.285 Chirality : 0.040 0.194 3288 Planarity : 0.003 0.027 3632 Dihedral : 4.504 21.895 2792 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 6.21 % Allowed : 25.58 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2496 helix: 1.11 (0.13), residues: 1680 sheet: -3.76 (0.40), residues: 80 loop : -3.06 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 59 HIS 0.013 0.002 HIS D 50 PHE 0.016 0.001 PHE E 330 TYR 0.015 0.001 TYR F 301 ARG 0.010 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 757 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.6250 (p0) cc_final: 0.6011 (p0) REVERT: A 67 GLN cc_start: 0.8219 (mp-120) cc_final: 0.7991 (mp10) REVERT: A 123 ARG cc_start: 0.8372 (ttm170) cc_final: 0.8078 (ttp-170) REVERT: A 153 ASP cc_start: 0.8543 (m-30) cc_final: 0.7875 (m-30) REVERT: A 154 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8359 (mtpt) REVERT: A 157 LYS cc_start: 0.8202 (tptt) cc_final: 0.7349 (ttpp) REVERT: A 158 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7454 (t80) REVERT: A 208 TYR cc_start: 0.8193 (t80) cc_final: 0.7525 (t80) REVERT: A 221 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5754 (pp) REVERT: A 305 LYS cc_start: 0.8543 (tttm) cc_final: 0.8231 (tmtt) REVERT: A 310 LYS cc_start: 0.7043 (ttpt) cc_final: 0.6427 (tptm) REVERT: A 353 PRO cc_start: 0.9396 (Cg_endo) cc_final: 0.9164 (Cg_exo) REVERT: B 105 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.6693 (m-10) REVERT: B 146 ARG cc_start: 0.8919 (ttp80) cc_final: 0.8335 (mtm110) REVERT: B 153 ASP cc_start: 0.8725 (m-30) cc_final: 0.8322 (m-30) REVERT: B 158 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7829 (t80) REVERT: B 161 ARG cc_start: 0.8148 (ttp-110) cc_final: 0.7945 (ttp-110) REVERT: B 170 SER cc_start: 0.9495 (t) cc_final: 0.9281 (m) REVERT: B 192 TYR cc_start: 0.8938 (t80) cc_final: 0.8729 (t80) REVERT: B 208 TYR cc_start: 0.8288 (t80) cc_final: 0.7959 (t80) REVERT: B 310 LYS cc_start: 0.7140 (ttpt) cc_final: 0.6495 (tptt) REVERT: B 322 LYS cc_start: 0.7815 (pttm) cc_final: 0.7112 (mptt) REVERT: B 359 ILE cc_start: 0.9467 (tp) cc_final: 0.9146 (tp) REVERT: C 123 ARG cc_start: 0.8400 (ttm170) cc_final: 0.8141 (ttp-170) REVERT: C 153 ASP cc_start: 0.8656 (m-30) cc_final: 0.8015 (m-30) REVERT: C 154 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8166 (mtpt) REVERT: C 157 LYS cc_start: 0.8286 (tptt) cc_final: 0.7700 (ttpp) REVERT: C 158 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7832 (t80) REVERT: C 208 TYR cc_start: 0.8257 (t80) cc_final: 0.7798 (t80) REVERT: C 305 LYS cc_start: 0.8471 (tttm) cc_final: 0.8138 (tmtt) REVERT: C 310 LYS cc_start: 0.6971 (ttpt) cc_final: 0.6244 (tptm) REVERT: C 322 LYS cc_start: 0.7513 (pttm) cc_final: 0.6793 (mptt) REVERT: C 359 ILE cc_start: 0.9399 (tp) cc_final: 0.9185 (tp) REVERT: D 65 ASN cc_start: 0.7420 (p0) cc_final: 0.7109 (p0) REVERT: D 105 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6999 (m-10) REVERT: D 146 ARG cc_start: 0.8908 (ttp80) cc_final: 0.8425 (mtm110) REVERT: D 158 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7434 (t80) REVERT: D 170 SER cc_start: 0.9391 (t) cc_final: 0.9175 (m) REVERT: D 192 TYR cc_start: 0.8932 (t80) cc_final: 0.8642 (t80) REVERT: D 208 TYR cc_start: 0.8365 (t80) cc_final: 0.8029 (t80) REVERT: D 274 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.6346 (mp0) REVERT: D 310 LYS cc_start: 0.7199 (ttpt) cc_final: 0.6860 (tptt) REVERT: D 322 LYS cc_start: 0.7664 (pttm) cc_final: 0.7020 (mptt) REVERT: D 332 SER cc_start: 0.9107 (m) cc_final: 0.8858 (t) REVERT: E 65 ASN cc_start: 0.6135 (p0) cc_final: 0.5911 (p0) REVERT: E 129 MET cc_start: 0.7421 (tpp) cc_final: 0.7084 (tpp) REVERT: E 157 LYS cc_start: 0.8423 (tptt) cc_final: 0.7824 (ttpp) REVERT: E 158 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7761 (t80) REVERT: E 206 GLN cc_start: 0.9289 (mm-40) cc_final: 0.8580 (mm-40) REVERT: E 208 TYR cc_start: 0.8114 (t80) cc_final: 0.7659 (t80) REVERT: E 305 LYS cc_start: 0.8437 (tttm) cc_final: 0.8067 (tmtt) REVERT: E 310 LYS cc_start: 0.7075 (ttpt) cc_final: 0.6643 (tptt) REVERT: E 322 LYS cc_start: 0.7445 (pttm) cc_final: 0.6471 (mptt) REVERT: E 353 PRO cc_start: 0.9404 (Cg_endo) cc_final: 0.9167 (Cg_exo) REVERT: F 65 ASN cc_start: 0.6919 (p0) cc_final: 0.6576 (p0) REVERT: F 105 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.7085 (m-10) REVERT: F 153 ASP cc_start: 0.8705 (m-30) cc_final: 0.8204 (m-30) REVERT: F 157 LYS cc_start: 0.8266 (tptt) cc_final: 0.7616 (ttmm) REVERT: F 158 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7599 (t80) REVERT: F 236 TRP cc_start: 0.8588 (p-90) cc_final: 0.8081 (p-90) REVERT: F 244 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7818 (mtt-85) REVERT: F 274 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.6367 (mp0) REVERT: F 304 ASN cc_start: 0.8598 (t0) cc_final: 0.8059 (t0) REVERT: F 310 LYS cc_start: 0.7201 (ttpt) cc_final: 0.6819 (tptt) REVERT: F 322 LYS cc_start: 0.7790 (pttm) cc_final: 0.7175 (mptt) REVERT: G 65 ASN cc_start: 0.6326 (p0) cc_final: 0.6038 (p0) REVERT: G 123 ARG cc_start: 0.8375 (ttm170) cc_final: 0.8119 (ttp-170) REVERT: G 154 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8212 (mtpt) REVERT: G 157 LYS cc_start: 0.8260 (tptt) cc_final: 0.7536 (ttpp) REVERT: G 170 SER cc_start: 0.9444 (m) cc_final: 0.9058 (m) REVERT: G 208 TYR cc_start: 0.8165 (t80) cc_final: 0.7721 (t80) REVERT: G 310 LYS cc_start: 0.7076 (ttpt) cc_final: 0.6408 (tptm) REVERT: G 322 LYS cc_start: 0.7373 (pttm) cc_final: 0.6656 (mptt) REVERT: G 353 PRO cc_start: 0.9416 (Cg_endo) cc_final: 0.9174 (Cg_exo) REVERT: H 105 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.7020 (m-10) REVERT: H 137 LEU cc_start: 0.9361 (tt) cc_final: 0.9147 (tt) REVERT: H 146 ARG cc_start: 0.8894 (ttp80) cc_final: 0.8311 (mtp-110) REVERT: H 153 ASP cc_start: 0.8628 (m-30) cc_final: 0.8196 (m-30) REVERT: H 157 LYS cc_start: 0.8294 (tptt) cc_final: 0.7911 (ttmm) REVERT: H 158 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7616 (t80) REVERT: H 192 TYR cc_start: 0.9129 (t80) cc_final: 0.8913 (t80) REVERT: H 208 TYR cc_start: 0.8413 (t80) cc_final: 0.8093 (t80) REVERT: H 305 LYS cc_start: 0.8542 (tttm) cc_final: 0.8327 (tmtt) REVERT: H 310 LYS cc_start: 0.7152 (ttpt) cc_final: 0.6527 (tptt) REVERT: H 313 LYS cc_start: 0.9300 (ttmt) cc_final: 0.9047 (ttmm) REVERT: H 322 LYS cc_start: 0.7786 (pttm) cc_final: 0.7160 (mptt) outliers start: 140 outliers final: 108 residues processed: 826 average time/residue: 0.3203 time to fit residues: 400.4334 Evaluate side-chains 863 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 740 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 187 ASN Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 187 ASN Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASN Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 332 SER Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.7980 chunk 222 optimal weight: 0.0670 chunk 48 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 247 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS B 67 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN G 67 GLN G 115 GLN G 270 ASN H 21 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21832 Z= 0.177 Angle : 0.571 12.144 29744 Z= 0.278 Chirality : 0.039 0.200 3288 Planarity : 0.003 0.027 3632 Dihedral : 4.399 22.392 2792 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 6.65 % Allowed : 25.58 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2496 helix: 1.20 (0.13), residues: 1680 sheet: -3.75 (0.39), residues: 80 loop : -3.01 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP H 236 HIS 0.015 0.001 HIS B 50 PHE 0.017 0.001 PHE G 330 TYR 0.015 0.001 TYR F 301 ARG 0.008 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 769 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8352 (ttm170) cc_final: 0.8064 (ttp-170) REVERT: A 153 ASP cc_start: 0.8553 (m-30) cc_final: 0.7972 (m-30) REVERT: A 154 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8339 (mtpt) REVERT: A 157 LYS cc_start: 0.8229 (tptt) cc_final: 0.7403 (ttpp) REVERT: A 158 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.7421 (t80) REVERT: A 208 TYR cc_start: 0.8180 (t80) cc_final: 0.7714 (t80) REVERT: A 221 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5988 (pp) REVERT: A 274 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.6196 (mp0) REVERT: A 305 LYS cc_start: 0.8539 (tttm) cc_final: 0.8214 (tmtt) REVERT: A 310 LYS cc_start: 0.7030 (ttpt) cc_final: 0.6402 (tptm) REVERT: A 345 MET cc_start: 0.9270 (tpp) cc_final: 0.8912 (tpp) REVERT: A 353 PRO cc_start: 0.9366 (Cg_endo) cc_final: 0.9145 (Cg_exo) REVERT: B 105 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6712 (m-10) REVERT: B 146 ARG cc_start: 0.8920 (ttp80) cc_final: 0.8317 (mtm110) REVERT: B 153 ASP cc_start: 0.8706 (m-30) cc_final: 0.8342 (m-30) REVERT: B 158 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7749 (t80) REVERT: B 170 SER cc_start: 0.9467 (t) cc_final: 0.9236 (m) REVERT: B 208 TYR cc_start: 0.8415 (t80) cc_final: 0.8086 (t80) REVERT: B 274 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: B 310 LYS cc_start: 0.7212 (ttpt) cc_final: 0.6581 (tptt) REVERT: B 315 TYR cc_start: 0.8244 (m-10) cc_final: 0.7478 (m-10) REVERT: B 322 LYS cc_start: 0.7783 (pttm) cc_final: 0.7130 (mptt) REVERT: B 359 ILE cc_start: 0.9462 (tp) cc_final: 0.9151 (tp) REVERT: C 153 ASP cc_start: 0.8652 (m-30) cc_final: 0.8020 (m-30) REVERT: C 154 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8230 (mtpt) REVERT: C 157 LYS cc_start: 0.8280 (tptt) cc_final: 0.7687 (ttpp) REVERT: C 158 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7851 (t80) REVERT: C 208 TYR cc_start: 0.8236 (t80) cc_final: 0.7785 (t80) REVERT: C 305 LYS cc_start: 0.8520 (tttm) cc_final: 0.8210 (tmtt) REVERT: C 310 LYS cc_start: 0.7022 (ttpt) cc_final: 0.6297 (tptm) REVERT: C 322 LYS cc_start: 0.7481 (pttm) cc_final: 0.6782 (mptt) REVERT: C 359 ILE cc_start: 0.9409 (tp) cc_final: 0.9157 (tp) REVERT: D 65 ASN cc_start: 0.7286 (p0) cc_final: 0.6973 (p0) REVERT: D 105 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.7001 (m-10) REVERT: D 158 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7397 (t80) REVERT: D 192 TYR cc_start: 0.8899 (t80) cc_final: 0.8627 (t80) REVERT: D 208 TYR cc_start: 0.8332 (t80) cc_final: 0.7950 (t80) REVERT: D 274 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: D 310 LYS cc_start: 0.7182 (ttpt) cc_final: 0.6848 (tptt) REVERT: D 322 LYS cc_start: 0.7627 (pttm) cc_final: 0.7002 (mptt) REVERT: D 332 SER cc_start: 0.9100 (m) cc_final: 0.8864 (t) REVERT: E 65 ASN cc_start: 0.6017 (p0) cc_final: 0.5769 (p0) REVERT: E 129 MET cc_start: 0.7403 (tpp) cc_final: 0.7059 (tpp) REVERT: E 157 LYS cc_start: 0.8268 (tptt) cc_final: 0.7813 (ttmm) REVERT: E 158 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7838 (t80) REVERT: E 206 GLN cc_start: 0.9284 (mm-40) cc_final: 0.8546 (mm-40) REVERT: E 208 TYR cc_start: 0.8131 (t80) cc_final: 0.7684 (t80) REVERT: E 305 LYS cc_start: 0.8410 (tttm) cc_final: 0.8100 (tmtt) REVERT: E 310 LYS cc_start: 0.7036 (ttpt) cc_final: 0.6523 (tptt) REVERT: E 322 LYS cc_start: 0.7377 (pttm) cc_final: 0.6693 (mptt) REVERT: E 353 PRO cc_start: 0.9384 (Cg_endo) cc_final: 0.9159 (Cg_exo) REVERT: F 28 ASP cc_start: 0.7121 (m-30) cc_final: 0.6873 (m-30) REVERT: F 65 ASN cc_start: 0.6776 (p0) cc_final: 0.6163 (p0) REVERT: F 105 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.7111 (m-10) REVERT: F 157 LYS cc_start: 0.8309 (tptt) cc_final: 0.7644 (ttmm) REVERT: F 158 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7467 (t80) REVERT: F 236 TRP cc_start: 0.8527 (p-90) cc_final: 0.8221 (p-90) REVERT: F 244 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8383 (mtt-85) REVERT: F 274 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.6384 (mp0) REVERT: F 310 LYS cc_start: 0.7178 (ttpt) cc_final: 0.6809 (tptt) REVERT: F 322 LYS cc_start: 0.7754 (pttm) cc_final: 0.7158 (mptt) REVERT: G 153 ASP cc_start: 0.8677 (m-30) cc_final: 0.8412 (m-30) REVERT: G 154 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8129 (mtpt) REVERT: G 157 LYS cc_start: 0.8218 (tptt) cc_final: 0.7605 (ttpp) REVERT: G 208 TYR cc_start: 0.8151 (t80) cc_final: 0.7703 (t80) REVERT: G 274 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: G 310 LYS cc_start: 0.7042 (ttpt) cc_final: 0.6405 (tptm) REVERT: G 322 LYS cc_start: 0.7327 (pttm) cc_final: 0.6709 (mptt) REVERT: G 353 PRO cc_start: 0.9392 (Cg_endo) cc_final: 0.9154 (Cg_exo) REVERT: H 47 LEU cc_start: 0.9479 (mm) cc_final: 0.9271 (mm) REVERT: H 105 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.7119 (m-10) REVERT: H 137 LEU cc_start: 0.9346 (tt) cc_final: 0.9142 (tt) REVERT: H 146 ARG cc_start: 0.8893 (ttp80) cc_final: 0.8283 (mtp-110) REVERT: H 153 ASP cc_start: 0.8613 (m-30) cc_final: 0.8196 (m-30) REVERT: H 157 LYS cc_start: 0.8286 (tptt) cc_final: 0.7845 (ttmm) REVERT: H 158 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7678 (t80) REVERT: H 192 TYR cc_start: 0.9118 (t80) cc_final: 0.8907 (t80) REVERT: H 206 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7595 (mp10) REVERT: H 208 TYR cc_start: 0.8404 (t80) cc_final: 0.8060 (t80) REVERT: H 274 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.6304 (mp0) REVERT: H 310 LYS cc_start: 0.7174 (ttpt) cc_final: 0.6573 (tptt) REVERT: H 313 LYS cc_start: 0.9311 (ttmt) cc_final: 0.9034 (ttmm) REVERT: H 315 TYR cc_start: 0.8290 (m-10) cc_final: 0.7548 (m-10) REVERT: H 322 LYS cc_start: 0.7794 (pttm) cc_final: 0.7137 (mptt) REVERT: H 359 ILE cc_start: 0.9473 (tp) cc_final: 0.9130 (tp) outliers start: 150 outliers final: 105 residues processed: 843 average time/residue: 0.3220 time to fit residues: 411.4539 Evaluate side-chains 866 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 741 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 187 ASN Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 187 ASN Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASN Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 332 SER Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 246 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 270 ASN B 50 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS C 206 GLN D 21 GLN D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN F 67 GLN G 67 GLN G 270 ASN H 21 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 21832 Z= 0.390 Angle : 0.675 12.506 29744 Z= 0.329 Chirality : 0.042 0.185 3288 Planarity : 0.003 0.026 3632 Dihedral : 4.633 23.452 2792 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 7.76 % Allowed : 25.58 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2496 helix: 1.01 (0.13), residues: 1696 sheet: -3.93 (0.38), residues: 80 loop : -3.02 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 236 HIS 0.015 0.002 HIS B 50 PHE 0.018 0.001 PHE B 242 TYR 0.017 0.002 TYR F 301 ARG 0.012 0.001 ARG G 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 731 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8418 (ttm170) cc_final: 0.8089 (ttp-170) REVERT: A 153 ASP cc_start: 0.8644 (m-30) cc_final: 0.7699 (m-30) REVERT: A 157 LYS cc_start: 0.8263 (tptt) cc_final: 0.7456 (ttpp) REVERT: A 208 TYR cc_start: 0.8186 (t80) cc_final: 0.7495 (t80) REVERT: A 274 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.6229 (mp0) REVERT: A 305 LYS cc_start: 0.8433 (tttm) cc_final: 0.8224 (tmtt) REVERT: A 310 LYS cc_start: 0.7061 (ttpt) cc_final: 0.6445 (tptm) REVERT: A 353 PRO cc_start: 0.9469 (Cg_endo) cc_final: 0.9225 (Cg_exo) REVERT: B 105 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.6796 (m-10) REVERT: B 146 ARG cc_start: 0.8953 (ttp80) cc_final: 0.8340 (mtm110) REVERT: B 153 ASP cc_start: 0.8756 (m-30) cc_final: 0.8376 (m-30) REVERT: B 208 TYR cc_start: 0.8456 (t80) cc_final: 0.8130 (t80) REVERT: B 274 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.6549 (mp0) REVERT: B 310 LYS cc_start: 0.7209 (ttpt) cc_final: 0.6569 (tptt) REVERT: B 322 LYS cc_start: 0.7852 (pttm) cc_final: 0.7155 (mptt) REVERT: B 359 ILE cc_start: 0.9499 (tp) cc_final: 0.9176 (tp) REVERT: C 153 ASP cc_start: 0.8671 (m-30) cc_final: 0.8070 (m-30) REVERT: C 154 LYS cc_start: 0.8892 (mtmt) cc_final: 0.8312 (mtpt) REVERT: C 157 LYS cc_start: 0.8325 (tptt) cc_final: 0.7745 (ttpp) REVERT: C 208 TYR cc_start: 0.8258 (t80) cc_final: 0.7581 (t80) REVERT: C 274 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: C 305 LYS cc_start: 0.8394 (tttm) cc_final: 0.8118 (tmtt) REVERT: C 310 LYS cc_start: 0.7015 (ttpt) cc_final: 0.6332 (tptm) REVERT: C 322 LYS cc_start: 0.7609 (pttm) cc_final: 0.6568 (mptt) REVERT: C 353 PRO cc_start: 0.9471 (Cg_endo) cc_final: 0.9236 (Cg_exo) REVERT: C 359 ILE cc_start: 0.9463 (tp) cc_final: 0.9203 (tp) REVERT: D 65 ASN cc_start: 0.7526 (p0) cc_final: 0.7195 (p0) REVERT: D 146 ARG cc_start: 0.8950 (ttp80) cc_final: 0.8463 (mtm110) REVERT: D 153 ASP cc_start: 0.8749 (m-30) cc_final: 0.8358 (m-30) REVERT: D 158 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7493 (t80) REVERT: D 192 TYR cc_start: 0.8963 (t80) cc_final: 0.8684 (t80) REVERT: D 208 TYR cc_start: 0.8377 (t80) cc_final: 0.8027 (t80) REVERT: D 229 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: D 274 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.6547 (mp0) REVERT: D 310 LYS cc_start: 0.7117 (ttpt) cc_final: 0.6730 (tptt) REVERT: D 322 LYS cc_start: 0.7705 (pttm) cc_final: 0.7043 (mptt) REVERT: E 65 ASN cc_start: 0.6384 (p0) cc_final: 0.6135 (p0) REVERT: E 129 MET cc_start: 0.7466 (tpp) cc_final: 0.7122 (tpp) REVERT: E 157 LYS cc_start: 0.8388 (tptt) cc_final: 0.7795 (ttpp) REVERT: E 158 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7981 (t80) REVERT: E 206 GLN cc_start: 0.9293 (mm-40) cc_final: 0.8450 (mm-40) REVERT: E 208 TYR cc_start: 0.8124 (t80) cc_final: 0.7475 (t80) REVERT: E 274 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: E 305 LYS cc_start: 0.8445 (tttm) cc_final: 0.8102 (tmtt) REVERT: E 310 LYS cc_start: 0.7136 (ttpt) cc_final: 0.6731 (tptm) REVERT: E 322 LYS cc_start: 0.7540 (pttm) cc_final: 0.6489 (mptt) REVERT: E 353 PRO cc_start: 0.9460 (Cg_endo) cc_final: 0.9227 (Cg_exo) REVERT: F 65 ASN cc_start: 0.6792 (p0) cc_final: 0.6243 (p0) REVERT: F 153 ASP cc_start: 0.8729 (m-30) cc_final: 0.8255 (m-30) REVERT: F 158 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7595 (t80) REVERT: F 244 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8158 (mtt-85) REVERT: F 274 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.6493 (mp0) REVERT: F 310 LYS cc_start: 0.7276 (ttpt) cc_final: 0.6870 (tptt) REVERT: G 154 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8184 (mtpt) REVERT: G 157 LYS cc_start: 0.8183 (tptt) cc_final: 0.7602 (ttpp) REVERT: G 208 TYR cc_start: 0.8192 (t80) cc_final: 0.7543 (t80) REVERT: G 212 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8143 (tp40) REVERT: G 274 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: G 310 LYS cc_start: 0.7125 (ttpt) cc_final: 0.6587 (tptt) REVERT: G 322 LYS cc_start: 0.7544 (pttm) cc_final: 0.6495 (mptt) REVERT: G 353 PRO cc_start: 0.9467 (Cg_endo) cc_final: 0.9219 (Cg_exo) REVERT: H 146 ARG cc_start: 0.8942 (ttp80) cc_final: 0.8349 (mtp-110) REVERT: H 153 ASP cc_start: 0.8679 (m-30) cc_final: 0.8266 (m-30) REVERT: H 158 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7776 (t80) REVERT: H 192 TYR cc_start: 0.9161 (t80) cc_final: 0.8904 (t80) REVERT: H 206 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.7467 (mp10) REVERT: H 208 TYR cc_start: 0.8436 (t80) cc_final: 0.8114 (t80) REVERT: H 274 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: H 310 LYS cc_start: 0.7210 (ttpt) cc_final: 0.6588 (tptt) REVERT: H 313 LYS cc_start: 0.9320 (ttmt) cc_final: 0.9073 (ttmm) REVERT: H 322 LYS cc_start: 0.7895 (pttm) cc_final: 0.7177 (mptt) outliers start: 175 outliers final: 140 residues processed: 822 average time/residue: 0.3175 time to fit residues: 396.5169 Evaluate side-chains 880 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 724 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 187 ASN Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 187 ASN Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 244 ARG Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASN Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 332 SER Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN B 50 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN F 67 GLN F 206 GLN G 67 GLN G 270 ASN ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21832 Z= 0.173 Angle : 0.603 12.531 29744 Z= 0.291 Chirality : 0.039 0.190 3288 Planarity : 0.003 0.027 3632 Dihedral : 4.407 22.151 2792 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 5.76 % Allowed : 27.57 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2496 helix: 1.22 (0.13), residues: 1688 sheet: -3.92 (0.37), residues: 80 loop : -3.04 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP A 236 HIS 0.020 0.002 HIS B 50 PHE 0.019 0.001 PHE A 330 TYR 0.022 0.001 TYR B 300 ARG 0.010 0.000 ARG G 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 776 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6864 (m-30) cc_final: 0.6580 (m-30) REVERT: A 123 ARG cc_start: 0.8361 (ttm170) cc_final: 0.8074 (ttp-170) REVERT: A 153 ASP cc_start: 0.8578 (m-30) cc_final: 0.7977 (m-30) REVERT: A 157 LYS cc_start: 0.8232 (tptt) cc_final: 0.7426 (ttpp) REVERT: A 206 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8847 (mm-40) REVERT: A 208 TYR cc_start: 0.8132 (t80) cc_final: 0.7708 (t80) REVERT: A 236 TRP cc_start: 0.8133 (p-90) cc_final: 0.7522 (p-90) REVERT: A 304 ASN cc_start: 0.8587 (t0) cc_final: 0.8372 (t0) REVERT: A 310 LYS cc_start: 0.6979 (ttpt) cc_final: 0.6405 (tptm) REVERT: A 353 PRO cc_start: 0.9352 (Cg_endo) cc_final: 0.9119 (Cg_exo) REVERT: B 105 TYR cc_start: 0.7172 (OUTLIER) cc_final: 0.6755 (m-10) REVERT: B 146 ARG cc_start: 0.8901 (ttp80) cc_final: 0.8389 (mtp-110) REVERT: B 153 ASP cc_start: 0.8713 (m-30) cc_final: 0.8380 (m-30) REVERT: B 170 SER cc_start: 0.9488 (t) cc_final: 0.9237 (m) REVERT: B 208 TYR cc_start: 0.8414 (t80) cc_final: 0.8072 (t80) REVERT: B 274 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: B 310 LYS cc_start: 0.7221 (ttpt) cc_final: 0.6601 (tptt) REVERT: B 315 TYR cc_start: 0.8229 (m-10) cc_final: 0.7450 (m-10) REVERT: B 322 LYS cc_start: 0.7826 (pttm) cc_final: 0.7131 (mptt) REVERT: B 359 ILE cc_start: 0.9455 (tp) cc_final: 0.9168 (tp) REVERT: C 153 ASP cc_start: 0.8641 (m-30) cc_final: 0.8110 (m-30) REVERT: C 157 LYS cc_start: 0.8322 (tptt) cc_final: 0.7863 (ttmm) REVERT: C 208 TYR cc_start: 0.8207 (t80) cc_final: 0.7735 (t80) REVERT: C 274 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: C 305 LYS cc_start: 0.8411 (tttm) cc_final: 0.8156 (tmtt) REVERT: C 310 LYS cc_start: 0.7034 (ttpt) cc_final: 0.6326 (tptm) REVERT: C 322 LYS cc_start: 0.7409 (pttm) cc_final: 0.6726 (mptt) REVERT: C 359 ILE cc_start: 0.9426 (tp) cc_final: 0.9169 (tp) REVERT: D 65 ASN cc_start: 0.7270 (p0) cc_final: 0.6942 (p0) REVERT: D 153 ASP cc_start: 0.8719 (m-30) cc_final: 0.8321 (m-30) REVERT: D 158 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7572 (t80) REVERT: D 192 TYR cc_start: 0.8902 (t80) cc_final: 0.8653 (t80) REVERT: D 208 TYR cc_start: 0.8304 (t80) cc_final: 0.7936 (t80) REVERT: D 274 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: D 310 LYS cc_start: 0.7145 (ttpt) cc_final: 0.6781 (tptt) REVERT: D 322 LYS cc_start: 0.7625 (pttm) cc_final: 0.7002 (mptt) REVERT: D 332 SER cc_start: 0.8999 (m) cc_final: 0.8723 (p) REVERT: E 105 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6970 (m-10) REVERT: E 157 LYS cc_start: 0.8414 (tptt) cc_final: 0.7684 (ttpp) REVERT: E 158 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7817 (t80) REVERT: E 206 GLN cc_start: 0.9298 (mm-40) cc_final: 0.8537 (mm-40) REVERT: E 208 TYR cc_start: 0.8135 (t80) cc_final: 0.7683 (t80) REVERT: E 274 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.6611 (mp0) REVERT: E 310 LYS cc_start: 0.7035 (ttpt) cc_final: 0.6537 (tptt) REVERT: E 322 LYS cc_start: 0.7370 (pttm) cc_final: 0.6692 (mptt) REVERT: E 345 MET cc_start: 0.9177 (tpp) cc_final: 0.8817 (tpp) REVERT: E 353 PRO cc_start: 0.9346 (Cg_endo) cc_final: 0.9115 (Cg_exo) REVERT: F 158 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7532 (t80) REVERT: F 274 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.6403 (mp0) REVERT: F 310 LYS cc_start: 0.7203 (ttpt) cc_final: 0.6830 (tptt) REVERT: F 322 LYS cc_start: 0.7760 (pttm) cc_final: 0.7136 (mptt) REVERT: G 153 ASP cc_start: 0.8695 (m-30) cc_final: 0.8425 (m-30) REVERT: G 154 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8178 (mtpt) REVERT: G 157 LYS cc_start: 0.8253 (tptt) cc_final: 0.7483 (ttpp) REVERT: G 158 PHE cc_start: 0.7593 (t80) cc_final: 0.7346 (t80) REVERT: G 208 TYR cc_start: 0.8173 (t80) cc_final: 0.7701 (t80) REVERT: G 274 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: G 310 LYS cc_start: 0.7020 (ttpt) cc_final: 0.6418 (tptm) REVERT: G 322 LYS cc_start: 0.7361 (pttm) cc_final: 0.6654 (mptt) REVERT: G 353 PRO cc_start: 0.9355 (Cg_endo) cc_final: 0.9106 (Cg_exo) REVERT: H 28 ASP cc_start: 0.7072 (m-30) cc_final: 0.6827 (m-30) REVERT: H 146 ARG cc_start: 0.8896 (ttp80) cc_final: 0.8274 (mtp-110) REVERT: H 153 ASP cc_start: 0.8635 (m-30) cc_final: 0.8214 (m-30) REVERT: H 158 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7648 (t80) REVERT: H 192 TYR cc_start: 0.9104 (t80) cc_final: 0.8868 (t80) REVERT: H 206 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.7601 (mp10) REVERT: H 208 TYR cc_start: 0.8387 (t80) cc_final: 0.8057 (t80) REVERT: H 236 TRP cc_start: 0.8488 (p-90) cc_final: 0.8271 (p-90) REVERT: H 274 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.6345 (mp0) REVERT: H 310 LYS cc_start: 0.7169 (ttpt) cc_final: 0.6606 (tptt) REVERT: H 313 LYS cc_start: 0.9289 (ttmt) cc_final: 0.9024 (ttmm) REVERT: H 315 TYR cc_start: 0.8261 (m-10) cc_final: 0.7538 (m-10) REVERT: H 322 LYS cc_start: 0.7827 (pttm) cc_final: 0.7150 (mptt) outliers start: 130 outliers final: 98 residues processed: 847 average time/residue: 0.3160 time to fit residues: 410.5459 Evaluate side-chains 853 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 741 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 187 ASN Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 187 ASN Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASN Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 332 SER Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 215 optimal weight: 0.0970 chunk 229 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS B 151 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS C 206 GLN D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN F 206 GLN G 270 ASN H 79 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21832 Z= 0.172 Angle : 0.622 13.251 29744 Z= 0.297 Chirality : 0.039 0.186 3288 Planarity : 0.003 0.027 3632 Dihedral : 4.318 22.394 2792 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 5.67 % Allowed : 28.19 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2496 helix: 1.25 (0.13), residues: 1696 sheet: -3.89 (0.38), residues: 80 loop : -2.90 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 236 HIS 0.017 0.002 HIS B 50 PHE 0.029 0.001 PHE H 124 TYR 0.023 0.001 TYR H 300 ARG 0.009 0.000 ARG G 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 767 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8349 (ttm170) cc_final: 0.8060 (ttp-170) REVERT: A 153 ASP cc_start: 0.8546 (m-30) cc_final: 0.8321 (m-30) REVERT: A 206 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8815 (mm-40) REVERT: A 208 TYR cc_start: 0.8126 (t80) cc_final: 0.7682 (t80) REVERT: A 236 TRP cc_start: 0.7967 (p-90) cc_final: 0.7244 (p-90) REVERT: A 274 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: A 304 ASN cc_start: 0.8602 (t0) cc_final: 0.8364 (t0) REVERT: A 305 LYS cc_start: 0.8421 (tmtt) cc_final: 0.8213 (tttm) REVERT: A 310 LYS cc_start: 0.6973 (ttpt) cc_final: 0.6427 (tptm) REVERT: A 345 MET cc_start: 0.9246 (tpp) cc_final: 0.8854 (tpp) REVERT: A 353 PRO cc_start: 0.9257 (Cg_endo) cc_final: 0.9026 (Cg_exo) REVERT: B 105 TYR cc_start: 0.7167 (OUTLIER) cc_final: 0.6765 (m-10) REVERT: B 146 ARG cc_start: 0.8898 (ttp80) cc_final: 0.8324 (mtm110) REVERT: B 153 ASP cc_start: 0.8711 (m-30) cc_final: 0.8360 (m-30) REVERT: B 170 SER cc_start: 0.9417 (t) cc_final: 0.9181 (m) REVERT: B 208 TYR cc_start: 0.8390 (t80) cc_final: 0.8060 (t80) REVERT: B 274 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.6495 (mp0) REVERT: B 310 LYS cc_start: 0.7198 (ttpt) cc_final: 0.6577 (tptm) REVERT: B 315 TYR cc_start: 0.8200 (m-10) cc_final: 0.7471 (m-10) REVERT: B 322 LYS cc_start: 0.7780 (pttm) cc_final: 0.7107 (mptt) REVERT: B 359 ILE cc_start: 0.9430 (tp) cc_final: 0.9131 (tp) REVERT: C 153 ASP cc_start: 0.8638 (m-30) cc_final: 0.8202 (m-30) REVERT: C 157 LYS cc_start: 0.8312 (tptt) cc_final: 0.7898 (ttmm) REVERT: C 208 TYR cc_start: 0.8204 (t80) cc_final: 0.7734 (t80) REVERT: C 274 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: C 310 LYS cc_start: 0.7043 (ttpt) cc_final: 0.6382 (tptm) REVERT: C 322 LYS cc_start: 0.7389 (pttm) cc_final: 0.6706 (mptt) REVERT: C 359 ILE cc_start: 0.9414 (tp) cc_final: 0.9152 (tp) REVERT: D 28 ASP cc_start: 0.7139 (m-30) cc_final: 0.6915 (m-30) REVERT: D 65 ASN cc_start: 0.7269 (p0) cc_final: 0.6921 (p0) REVERT: D 153 ASP cc_start: 0.8692 (m-30) cc_final: 0.8309 (m-30) REVERT: D 158 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7587 (t80) REVERT: D 192 TYR cc_start: 0.8889 (t80) cc_final: 0.8644 (t80) REVERT: D 208 TYR cc_start: 0.8297 (t80) cc_final: 0.7905 (t80) REVERT: D 274 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.6418 (mp0) REVERT: D 310 LYS cc_start: 0.7187 (ttpt) cc_final: 0.6814 (tptt) REVERT: D 322 LYS cc_start: 0.7565 (pttm) cc_final: 0.6940 (mptt) REVERT: D 359 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9204 (tp) REVERT: E 153 ASP cc_start: 0.8686 (m-30) cc_final: 0.8400 (m-30) REVERT: E 157 LYS cc_start: 0.8330 (tptt) cc_final: 0.7605 (ttmm) REVERT: E 158 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7775 (t80) REVERT: E 175 ASP cc_start: 0.8124 (m-30) cc_final: 0.7592 (m-30) REVERT: E 206 GLN cc_start: 0.9276 (mm-40) cc_final: 0.8505 (mm-40) REVERT: E 208 TYR cc_start: 0.8166 (t80) cc_final: 0.7721 (t80) REVERT: E 274 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: E 310 LYS cc_start: 0.7035 (ttpt) cc_final: 0.6544 (tptt) REVERT: E 322 LYS cc_start: 0.7292 (pttm) cc_final: 0.6455 (tttm) REVERT: E 353 PRO cc_start: 0.9259 (Cg_endo) cc_final: 0.9041 (Cg_exo) REVERT: F 28 ASP cc_start: 0.7118 (m-30) cc_final: 0.6846 (m-30) REVERT: F 158 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7451 (t80) REVERT: F 274 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.6407 (mp0) REVERT: F 310 LYS cc_start: 0.7271 (ttpt) cc_final: 0.6893 (tptt) REVERT: F 322 LYS cc_start: 0.7679 (pttm) cc_final: 0.7040 (mptt) REVERT: G 153 ASP cc_start: 0.8681 (m-30) cc_final: 0.8442 (m-30) REVERT: G 157 LYS cc_start: 0.8253 (tptt) cc_final: 0.7248 (ttmm) REVERT: G 158 PHE cc_start: 0.7515 (t80) cc_final: 0.7277 (t80) REVERT: G 208 TYR cc_start: 0.8162 (t80) cc_final: 0.7702 (t80) REVERT: G 274 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.6494 (mp0) REVERT: G 310 LYS cc_start: 0.6993 (ttpt) cc_final: 0.6408 (tptm) REVERT: G 322 LYS cc_start: 0.7286 (pttm) cc_final: 0.6635 (mptt) REVERT: G 353 PRO cc_start: 0.9261 (Cg_endo) cc_final: 0.9032 (Cg_exo) REVERT: H 130 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8805 (tp) REVERT: H 153 ASP cc_start: 0.8652 (m-30) cc_final: 0.8256 (m-30) REVERT: H 158 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7538 (t80) REVERT: H 192 TYR cc_start: 0.9099 (t80) cc_final: 0.8875 (t80) REVERT: H 206 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7565 (mp10) REVERT: H 208 TYR cc_start: 0.8384 (t80) cc_final: 0.8030 (t80) REVERT: H 274 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.6288 (mp0) REVERT: H 310 LYS cc_start: 0.7230 (ttpt) cc_final: 0.6661 (tptt) REVERT: H 313 LYS cc_start: 0.9273 (ttmt) cc_final: 0.8945 (ttmm) REVERT: H 315 TYR cc_start: 0.8252 (m-10) cc_final: 0.7525 (m-10) REVERT: H 316 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8497 (mm) REVERT: H 322 LYS cc_start: 0.7785 (pttm) cc_final: 0.7148 (mptt) outliers start: 128 outliers final: 103 residues processed: 829 average time/residue: 0.3040 time to fit residues: 387.7758 Evaluate side-chains 854 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 734 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 187 ASN Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 187 ASN Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 270 ASN Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASN Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 332 SER Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 169 optimal weight: 0.0070 chunk 255 optimal weight: 0.9990 chunk 234 optimal weight: 8.9990 chunk 203 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS B 151 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS C 115 GLN D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 ASN G 67 GLN ** G 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21832 Z= 0.193 Angle : 0.635 13.484 29744 Z= 0.304 Chirality : 0.039 0.179 3288 Planarity : 0.003 0.028 3632 Dihedral : 4.275 22.753 2792 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 5.54 % Allowed : 28.90 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.18), residues: 2496 helix: 1.28 (0.13), residues: 1696 sheet: None (None), residues: 0 loop : -2.81 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B 236 HIS 0.020 0.002 HIS C 50 PHE 0.020 0.001 PHE E 330 TYR 0.022 0.001 TYR H 300 ARG 0.009 0.000 ARG G 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 746 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.8349 (ttm170) cc_final: 0.8073 (ttp-170) REVERT: A 153 ASP cc_start: 0.8582 (m-30) cc_final: 0.8359 (m-30) REVERT: A 206 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8801 (mm-40) REVERT: A 208 TYR cc_start: 0.8138 (t80) cc_final: 0.7692 (t80) REVERT: A 236 TRP cc_start: 0.7924 (p-90) cc_final: 0.7302 (p-90) REVERT: A 274 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: A 304 ASN cc_start: 0.8618 (t0) cc_final: 0.8381 (t0) REVERT: A 310 LYS cc_start: 0.6982 (ttpt) cc_final: 0.6439 (tptm) REVERT: A 353 PRO cc_start: 0.9241 (Cg_endo) cc_final: 0.9019 (Cg_exo) REVERT: B 28 ASP cc_start: 0.7035 (m-30) cc_final: 0.6780 (m-30) REVERT: B 105 TYR cc_start: 0.7216 (OUTLIER) cc_final: 0.6820 (m-10) REVERT: B 146 ARG cc_start: 0.8880 (ttp80) cc_final: 0.8345 (mtm110) REVERT: B 153 ASP cc_start: 0.8689 (m-30) cc_final: 0.8361 (m-30) REVERT: B 170 SER cc_start: 0.9420 (t) cc_final: 0.9187 (m) REVERT: B 208 TYR cc_start: 0.8404 (t80) cc_final: 0.8073 (t80) REVERT: B 274 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.6440 (mp0) REVERT: B 310 LYS cc_start: 0.7207 (ttpt) cc_final: 0.6602 (tptm) REVERT: B 315 TYR cc_start: 0.8202 (m-10) cc_final: 0.7500 (m-10) REVERT: B 322 LYS cc_start: 0.7765 (pttm) cc_final: 0.7111 (mptt) REVERT: B 359 ILE cc_start: 0.9462 (tp) cc_final: 0.9176 (tp) REVERT: C 153 ASP cc_start: 0.8583 (m-30) cc_final: 0.8151 (m-30) REVERT: C 157 LYS cc_start: 0.8297 (tptt) cc_final: 0.7794 (ttmm) REVERT: C 208 TYR cc_start: 0.8185 (t80) cc_final: 0.7715 (t80) REVERT: C 274 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: C 304 ASN cc_start: 0.8565 (t0) cc_final: 0.8348 (t0) REVERT: C 310 LYS cc_start: 0.7046 (ttpt) cc_final: 0.6398 (tptm) REVERT: C 322 LYS cc_start: 0.7352 (pttm) cc_final: 0.6685 (mptt) REVERT: C 359 ILE cc_start: 0.9415 (tp) cc_final: 0.9153 (tp) REVERT: D 28 ASP cc_start: 0.7121 (m-30) cc_final: 0.6827 (m-30) REVERT: D 65 ASN cc_start: 0.7259 (p0) cc_final: 0.6888 (p0) REVERT: D 153 ASP cc_start: 0.8683 (m-30) cc_final: 0.8285 (m-30) REVERT: D 158 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7596 (t80) REVERT: D 192 TYR cc_start: 0.8895 (t80) cc_final: 0.8658 (t80) REVERT: D 208 TYR cc_start: 0.8305 (t80) cc_final: 0.7924 (t80) REVERT: D 274 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.6283 (mp0) REVERT: D 310 LYS cc_start: 0.7196 (ttpt) cc_final: 0.6853 (tptt) REVERT: D 322 LYS cc_start: 0.7576 (pttm) cc_final: 0.6950 (mptt) REVERT: E 153 ASP cc_start: 0.8643 (m-30) cc_final: 0.8374 (m-30) REVERT: E 157 LYS cc_start: 0.8309 (tptt) cc_final: 0.7575 (ttmm) REVERT: E 158 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7718 (t80) REVERT: E 175 ASP cc_start: 0.8126 (m-30) cc_final: 0.7594 (m-30) REVERT: E 206 GLN cc_start: 0.9266 (mm-40) cc_final: 0.8951 (mm-40) REVERT: E 208 TYR cc_start: 0.8176 (t80) cc_final: 0.7713 (t80) REVERT: E 274 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: E 310 LYS cc_start: 0.7006 (ttpt) cc_final: 0.6514 (tptt) REVERT: E 322 LYS cc_start: 0.7281 (pttm) cc_final: 0.6451 (tttm) REVERT: E 353 PRO cc_start: 0.9268 (Cg_endo) cc_final: 0.9035 (Cg_exo) REVERT: F 28 ASP cc_start: 0.7108 (m-30) cc_final: 0.6826 (m-30) REVERT: F 158 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7646 (t80) REVERT: F 274 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: F 310 LYS cc_start: 0.7278 (ttpt) cc_final: 0.6904 (tptt) REVERT: F 322 LYS cc_start: 0.7668 (pttm) cc_final: 0.7030 (mptt) REVERT: G 153 ASP cc_start: 0.8658 (m-30) cc_final: 0.8435 (m-30) REVERT: G 157 LYS cc_start: 0.8251 (tptt) cc_final: 0.7179 (ttmm) REVERT: G 158 PHE cc_start: 0.7529 (t80) cc_final: 0.7294 (t80) REVERT: G 208 TYR cc_start: 0.8172 (t80) cc_final: 0.7708 (t80) REVERT: G 274 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: G 305 LYS cc_start: 0.8600 (tmtt) cc_final: 0.8390 (tmtt) REVERT: G 310 LYS cc_start: 0.7001 (ttpt) cc_final: 0.6424 (tptm) REVERT: G 322 LYS cc_start: 0.7279 (pttm) cc_final: 0.6624 (mptt) REVERT: G 353 PRO cc_start: 0.9275 (Cg_endo) cc_final: 0.9024 (Cg_exo) REVERT: H 28 ASP cc_start: 0.7054 (m-30) cc_final: 0.6788 (m-30) REVERT: H 130 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8810 (tp) REVERT: H 153 ASP cc_start: 0.8657 (m-30) cc_final: 0.8285 (m-30) REVERT: H 158 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7493 (t80) REVERT: H 192 TYR cc_start: 0.9095 (t80) cc_final: 0.8866 (t80) REVERT: H 206 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7520 (mp10) REVERT: H 208 TYR cc_start: 0.8391 (t80) cc_final: 0.8044 (t80) REVERT: H 274 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.6204 (mp0) REVERT: H 310 LYS cc_start: 0.7241 (ttpt) cc_final: 0.6679 (tptt) REVERT: H 313 LYS cc_start: 0.9275 (ttmt) cc_final: 0.8942 (ttmm) REVERT: H 315 TYR cc_start: 0.8261 (m-10) cc_final: 0.7556 (m-10) REVERT: H 316 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8494 (mm) REVERT: H 322 LYS cc_start: 0.7760 (pttm) cc_final: 0.7135 (mptt) outliers start: 125 outliers final: 101 residues processed: 812 average time/residue: 0.3105 time to fit residues: 391.1064 Evaluate side-chains 843 residues out of total 2288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 726 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 158 PHE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 187 ASN Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 158 PHE Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 187 ASN Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 332 SER Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 158 PHE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASN Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 285 VAL Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 332 SER Chi-restraints excluded: chain H residue 360 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 4.9990 chunk 62 optimal weight: 0.0670 chunk 187 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 208 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 overall best weight: 1.2318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS C 115 GLN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN E 270 ASN ** G 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.110061 restraints weight = 31515.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.114024 restraints weight = 16588.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.116775 restraints weight = 10925.041| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21832 Z= 0.182 Angle : 0.636 13.302 29744 Z= 0.303 Chirality : 0.039 0.162 3288 Planarity : 0.003 0.029 3632 Dihedral : 4.262 22.478 2792 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 5.23 % Allowed : 29.88 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.18), residues: 2496 helix: 1.30 (0.13), residues: 1696 sheet: None (None), residues: 0 loop : -2.77 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 236 HIS 0.017 0.001 HIS D 50 PHE 0.019 0.001 PHE E 330 TYR 0.024 0.001 TYR B 300 ARG 0.009 0.000 ARG G 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6089.45 seconds wall clock time: 110 minutes 39.22 seconds (6639.22 seconds total)