Starting phenix.real_space_refine on Tue Apr 9 13:17:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vd7_21150/04_2024/6vd7_21150.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vd7_21150/04_2024/6vd7_21150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vd7_21150/04_2024/6vd7_21150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vd7_21150/04_2024/6vd7_21150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vd7_21150/04_2024/6vd7_21150.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vd7_21150/04_2024/6vd7_21150.pdb" } resolution = 3.02 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= 0.008 sd= 0.694 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 77 5.16 5 C 11088 2.51 5 N 2513 2.21 5 O 2828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 329": "OD1" <-> "OD2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 329": "OD1" <-> "OD2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 329": "OD1" <-> "OD2" Residue "C GLU 343": "OE1" <-> "OE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 329": "OD1" <-> "OD2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 329": "OD1" <-> "OD2" Residue "E GLU 343": "OE1" <-> "OE2" Residue "F PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 251": "NH1" <-> "NH2" Residue "F PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 329": "OD1" <-> "OD2" Residue "F GLU 343": "OE1" <-> "OE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 251": "NH1" <-> "NH2" Residue "G PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 329": "OD1" <-> "OD2" Residue "G GLU 343": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16506 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2358 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2358 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2358 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2358 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2358 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2358 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2358 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 8.77, per 1000 atoms: 0.53 Number of scatterers: 16506 At special positions: 0 Unit cell: (107, 109.14, 117.7, 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 77 16.00 O 2828 8.00 N 2513 7.00 C 11088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 267 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 267 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 267 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 267 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 267 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 267 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 267 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 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: 6.14 Conformation dependent library (CDL) restraints added in 2.4 seconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4060 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 7 sheets defined 69.4% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 33 through 61 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 84 removed outlier: 4.071A pdb=" N VAL A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 108 through 131 removed outlier: 3.671A pdb=" N LEU A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 154 Processing helix chain 'A' and resid 196 through 205 removed outlier: 3.621A pdb=" N LYS A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 241 removed outlier: 3.628A pdb=" N SER A 241 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 298 Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 299 through 302 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.703A pdb=" N LEU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 357 removed outlier: 4.279A pdb=" N PHE A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 61 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 84 removed outlier: 4.071A pdb=" N VAL B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 108 through 131 removed outlier: 3.671A pdb=" N LEU B 113 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 154 Processing helix chain 'B' and resid 196 through 205 removed outlier: 3.622A pdb=" N LYS B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 241 removed outlier: 3.628A pdb=" N SER B 241 " --> pdb=" O ILE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 298 Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 299 through 302 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.702A pdb=" N LEU B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 4.278A pdb=" N PHE B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 61 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 84 removed outlier: 4.072A pdb=" N VAL C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 108 through 131 removed outlier: 3.671A pdb=" N LEU C 113 " --> pdb=" O PHE C 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU C 114 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 154 Processing helix chain 'C' and resid 196 through 205 removed outlier: 3.621A pdb=" N LYS C 205 " --> pdb=" O TYR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 241 removed outlier: 3.628A pdb=" N SER C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 298 Proline residue: C 291 - end of helix Processing helix chain 'C' and resid 299 through 302 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 312 through 314 No H-bonds generated for 'chain 'C' and resid 312 through 314' Processing helix chain 'C' and resid 328 through 341 removed outlier: 3.702A pdb=" N LEU C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 357 removed outlier: 4.278A pdb=" N PHE C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 61 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 84 removed outlier: 4.071A pdb=" N VAL D 80 " --> pdb=" O GLN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 108 through 131 removed outlier: 3.671A pdb=" N LEU D 113 " --> pdb=" O PHE D 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU D 114 " --> pdb=" O PRO D 110 " (cutoff:3.500A) Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 154 Processing helix chain 'D' and resid 196 through 205 removed outlier: 3.621A pdb=" N LYS D 205 " --> pdb=" O TYR D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 241 removed outlier: 3.628A pdb=" N SER D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 298 Proline residue: D 291 - end of helix Processing helix chain 'D' and resid 299 through 302 Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'D' and resid 312 through 314 No H-bonds generated for 'chain 'D' and resid 312 through 314' Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.703A pdb=" N LEU D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 357 removed outlier: 4.278A pdb=" N PHE D 349 " --> pdb=" O LYS D 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 61 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 84 removed outlier: 4.071A pdb=" N VAL E 80 " --> pdb=" O GLN E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 108 through 131 removed outlier: 3.671A pdb=" N LEU E 113 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU E 114 " --> pdb=" O PRO E 110 " (cutoff:3.500A) Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 154 Processing helix chain 'E' and resid 196 through 205 removed outlier: 3.621A pdb=" N LYS E 205 " --> pdb=" O TYR E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 241 removed outlier: 3.627A pdb=" N SER E 241 " --> pdb=" O ILE E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 298 Proline residue: E 291 - end of helix Processing helix chain 'E' and resid 299 through 302 Processing helix chain 'E' and resid 306 through 311 Processing helix chain 'E' and resid 312 through 314 No H-bonds generated for 'chain 'E' and resid 312 through 314' Processing helix chain 'E' and resid 328 through 341 removed outlier: 3.703A pdb=" N LEU E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 357 removed outlier: 4.279A pdb=" N PHE E 349 " --> pdb=" O LYS E 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 61 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 84 removed outlier: 4.072A pdb=" N VAL F 80 " --> pdb=" O GLN F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 108 through 131 removed outlier: 3.671A pdb=" N LEU F 113 " --> pdb=" O PHE F 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU F 114 " --> pdb=" O PRO F 110 " (cutoff:3.500A) Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 154 Processing helix chain 'F' and resid 196 through 205 removed outlier: 3.621A pdb=" N LYS F 205 " --> pdb=" O TYR F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 241 removed outlier: 3.628A pdb=" N SER F 241 " --> pdb=" O ILE F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 298 Proline residue: F 291 - end of helix Processing helix chain 'F' and resid 299 through 302 Processing helix chain 'F' and resid 306 through 311 Processing helix chain 'F' and resid 312 through 314 No H-bonds generated for 'chain 'F' and resid 312 through 314' Processing helix chain 'F' and resid 328 through 341 removed outlier: 3.702A pdb=" N LEU F 332 " --> pdb=" O ASP F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 357 removed outlier: 4.279A pdb=" N PHE F 349 " --> pdb=" O LYS F 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 61 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 84 removed outlier: 4.071A pdb=" N VAL G 80 " --> pdb=" O GLN G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 108 Processing helix chain 'G' and resid 108 through 131 removed outlier: 3.671A pdb=" N LEU G 113 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU G 114 " --> pdb=" O PRO G 110 " (cutoff:3.500A) Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 154 Processing helix chain 'G' and resid 196 through 205 removed outlier: 3.622A pdb=" N LYS G 205 " --> pdb=" O TYR G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 241 removed outlier: 3.628A pdb=" N SER G 241 " --> pdb=" O ILE G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 298 Proline residue: G 291 - end of helix Processing helix chain 'G' and resid 299 through 302 Processing helix chain 'G' and resid 306 through 311 Processing helix chain 'G' and resid 312 through 314 No H-bonds generated for 'chain 'G' and resid 312 through 314' Processing helix chain 'G' and resid 328 through 341 removed outlier: 3.702A pdb=" N LEU G 332 " --> pdb=" O ASP G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 357 removed outlier: 4.278A pdb=" N PHE G 349 " --> pdb=" O LYS G 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 1022 hydrogen bonds defined for protein. 3024 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: 4.29 Time building geometry restraints manager: 6.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4815 1.34 - 1.46: 3531 1.46 - 1.57: 8496 1.57 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 16940 Sorted by residual: bond pdb=" CB THR C 59 " pdb=" CG2 THR C 59 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.73e+00 bond pdb=" CB THR E 59 " pdb=" CG2 THR E 59 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.72e+00 bond pdb=" CB THR B 59 " pdb=" CG2 THR B 59 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.72e+00 bond pdb=" CB THR A 59 " pdb=" CG2 THR A 59 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.71e+00 bond pdb=" CB THR F 59 " pdb=" CG2 THR F 59 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.71e+00 ... (remaining 16935 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.05: 497 107.05 - 113.78: 9724 113.78 - 120.52: 7064 120.52 - 127.25: 5675 127.25 - 133.98: 182 Bond angle restraints: 23142 Sorted by residual: angle pdb=" N VAL A 299 " pdb=" CA VAL A 299 " pdb=" C VAL A 299 " ideal model delta sigma weight residual 108.88 116.03 -7.15 2.16e+00 2.14e-01 1.10e+01 angle pdb=" N VAL D 299 " pdb=" CA VAL D 299 " pdb=" C VAL D 299 " ideal model delta sigma weight residual 108.88 116.03 -7.15 2.16e+00 2.14e-01 1.10e+01 angle pdb=" N VAL B 299 " pdb=" CA VAL B 299 " pdb=" C VAL B 299 " ideal model delta sigma weight residual 108.88 116.03 -7.15 2.16e+00 2.14e-01 1.09e+01 angle pdb=" N VAL G 299 " pdb=" CA VAL G 299 " pdb=" C VAL G 299 " ideal model delta sigma weight residual 108.88 116.02 -7.14 2.16e+00 2.14e-01 1.09e+01 angle pdb=" N VAL C 299 " pdb=" CA VAL C 299 " pdb=" C VAL C 299 " ideal model delta sigma weight residual 108.88 116.02 -7.14 2.16e+00 2.14e-01 1.09e+01 ... (remaining 23137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.11: 8325 12.11 - 24.22: 1083 24.22 - 36.32: 525 36.32 - 48.43: 42 48.43 - 60.54: 28 Dihedral angle restraints: 10003 sinusoidal: 3759 harmonic: 6244 Sorted by residual: dihedral pdb=" CA GLU B 22 " pdb=" C GLU B 22 " pdb=" N SER B 23 " pdb=" CA SER B 23 " ideal model delta harmonic sigma weight residual 180.00 149.34 30.66 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA GLU E 22 " pdb=" C GLU E 22 " pdb=" N SER E 23 " pdb=" CA SER E 23 " ideal model delta harmonic sigma weight residual 180.00 149.37 30.63 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" CA GLU A 22 " pdb=" C GLU A 22 " pdb=" N SER A 23 " pdb=" CA SER A 23 " ideal model delta harmonic sigma weight residual 180.00 149.40 30.60 0 5.00e+00 4.00e-02 3.75e+01 ... (remaining 10000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1556 0.032 - 0.065: 870 0.065 - 0.097: 205 0.097 - 0.129: 141 0.129 - 0.161: 21 Chirality restraints: 2793 Sorted by residual: chirality pdb=" CB THR C 59 " pdb=" CA THR C 59 " pdb=" OG1 THR C 59 " pdb=" CG2 THR C 59 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CB THR E 59 " pdb=" CA THR E 59 " pdb=" OG1 THR E 59 " pdb=" CG2 THR E 59 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CB THR B 59 " pdb=" CA THR B 59 " pdb=" OG1 THR B 59 " pdb=" CG2 THR B 59 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 2790 not shown) Planarity restraints: 2793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 33 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C ALA G 33 " -0.068 2.00e-02 2.50e+03 pdb=" O ALA G 33 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL G 34 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 33 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C ALA F 33 " 0.068 2.00e-02 2.50e+03 pdb=" O ALA F 33 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL F 34 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 33 " 0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C ALA C 33 " -0.068 2.00e-02 2.50e+03 pdb=" O ALA C 33 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL C 34 " 0.023 2.00e-02 2.50e+03 ... (remaining 2790 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4842 2.81 - 3.33: 15941 3.33 - 3.85: 25709 3.85 - 4.38: 29155 4.38 - 4.90: 51521 Nonbonded interactions: 127168 Sorted by model distance: nonbonded pdb=" O TYR C 201 " pdb=" OG1 THR C 204 " model vdw 2.284 2.440 nonbonded pdb=" O TYR A 201 " pdb=" OG1 THR A 204 " model vdw 2.284 2.440 nonbonded pdb=" O TYR D 201 " pdb=" OG1 THR D 204 " model vdw 2.284 2.440 nonbonded pdb=" O TYR E 201 " pdb=" OG1 THR E 204 " model vdw 2.284 2.440 nonbonded pdb=" O TYR G 201 " pdb=" OG1 THR G 204 " model vdw 2.284 2.440 ... (remaining 127163 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 4.630 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 41.470 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 16940 Z= 0.493 Angle : 0.765 7.149 23142 Z= 0.413 Chirality : 0.045 0.161 2793 Planarity : 0.004 0.040 2793 Dihedral : 13.380 60.537 5901 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 0.78 % Allowed : 6.17 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -2.54 (0.17), residues: 2037 helix: -0.17 (0.14), residues: 1260 sheet: -0.97 (0.48), residues: 84 loop : -4.80 (0.18), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 85 HIS 0.002 0.001 HIS F 330 PHE 0.017 0.002 PHE F 240 TYR 0.018 0.002 TYR E 25 ARG 0.002 0.000 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 315 time to evaluate : 2.028 Fit side-chains REVERT: A 54 PHE cc_start: 0.7966 (m-80) cc_final: 0.6638 (t80) REVERT: B 54 PHE cc_start: 0.8020 (m-80) cc_final: 0.7569 (m-80) REVERT: B 104 TRP cc_start: 0.7995 (p-90) cc_final: 0.7578 (p-90) REVERT: B 312 GLU cc_start: 0.7944 (pt0) cc_final: 0.7721 (pt0) REVERT: C 74 TRP cc_start: 0.7373 (t-100) cc_final: 0.7141 (t-100) REVERT: C 104 TRP cc_start: 0.7976 (p-90) cc_final: 0.7719 (p-90) REVERT: C 244 ASP cc_start: 0.7256 (p0) cc_final: 0.6915 (p0) REVERT: C 245 GLU cc_start: 0.7666 (pt0) cc_final: 0.7413 (pt0) REVERT: D 104 TRP cc_start: 0.7854 (p-90) cc_final: 0.7585 (p-90) REVERT: D 244 ASP cc_start: 0.7010 (p0) cc_final: 0.6753 (p0) REVERT: D 312 GLU cc_start: 0.7898 (pt0) cc_final: 0.7598 (pt0) REVERT: E 63 GLN cc_start: 0.7936 (mm110) cc_final: 0.7683 (mm-40) REVERT: E 74 TRP cc_start: 0.7375 (t-100) cc_final: 0.7092 (t-100) REVERT: E 327 TYR cc_start: 0.8678 (m-80) cc_final: 0.8218 (m-80) REVERT: F 54 PHE cc_start: 0.8068 (m-80) cc_final: 0.7839 (m-80) REVERT: F 63 GLN cc_start: 0.8075 (mm110) cc_final: 0.7738 (mm-40) REVERT: F 244 ASP cc_start: 0.7421 (p0) cc_final: 0.7213 (p0) REVERT: G 54 PHE cc_start: 0.8109 (m-80) cc_final: 0.6768 (t80) REVERT: G 63 GLN cc_start: 0.8095 (mm110) cc_final: 0.7797 (mm-40) REVERT: G 143 MET cc_start: 0.9035 (mtp) cc_final: 0.8825 (mtt) REVERT: G 312 GLU cc_start: 0.7959 (pt0) cc_final: 0.7542 (pt0) outliers start: 14 outliers final: 1 residues processed: 315 average time/residue: 0.2942 time to fit residues: 136.8732 Evaluate side-chains 226 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 59 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 184 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN B 207 ASN B 266 GLN C 63 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN C 207 ASN D 63 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN D 266 GLN D 282 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 ASN G 266 GLN G 282 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16940 Z= 0.182 Angle : 0.611 7.274 23142 Z= 0.315 Chirality : 0.040 0.182 2793 Planarity : 0.004 0.025 2793 Dihedral : 5.270 29.172 2241 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 2.22 % Allowed : 11.95 % Favored : 85.83 % 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: -0.61 (0.20), residues: 2037 helix: 1.30 (0.15), residues: 1302 sheet: -0.31 (0.54), residues: 84 loop : -4.21 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 74 HIS 0.003 0.001 HIS G 106 PHE 0.008 0.001 PHE A 240 TYR 0.012 0.001 TYR C 25 ARG 0.003 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 255 time to evaluate : 1.796 Fit side-chains REVERT: A 54 PHE cc_start: 0.7950 (m-80) cc_final: 0.6529 (t80) REVERT: A 244 ASP cc_start: 0.6859 (p0) cc_final: 0.6245 (p0) REVERT: B 54 PHE cc_start: 0.8036 (m-80) cc_final: 0.7739 (m-80) REVERT: B 104 TRP cc_start: 0.7778 (p-90) cc_final: 0.7496 (p-90) REVERT: C 104 TRP cc_start: 0.7825 (p-90) cc_final: 0.7476 (p-90) REVERT: C 244 ASP cc_start: 0.7076 (p0) cc_final: 0.6725 (p0) REVERT: D 104 TRP cc_start: 0.7793 (p-90) cc_final: 0.7505 (p-90) REVERT: D 244 ASP cc_start: 0.6807 (p0) cc_final: 0.6493 (p0) REVERT: D 312 GLU cc_start: 0.7692 (pt0) cc_final: 0.7388 (pt0) REVERT: D 354 GLU cc_start: 0.7957 (pp20) cc_final: 0.7714 (pp20) REVERT: E 244 ASP cc_start: 0.6952 (p0) cc_final: 0.6654 (p0) REVERT: E 310 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8462 (t) REVERT: E 327 TYR cc_start: 0.8537 (m-80) cc_final: 0.8128 (m-80) REVERT: F 54 PHE cc_start: 0.8041 (m-80) cc_final: 0.7743 (m-80) REVERT: F 244 ASP cc_start: 0.7093 (p0) cc_final: 0.6856 (p0) REVERT: G 54 PHE cc_start: 0.8136 (m-80) cc_final: 0.6784 (t80) REVERT: G 63 GLN cc_start: 0.8034 (mm110) cc_final: 0.7640 (mm-40) REVERT: G 104 TRP cc_start: 0.7822 (p-90) cc_final: 0.7574 (p-90) REVERT: G 312 GLU cc_start: 0.7821 (pt0) cc_final: 0.7509 (pt0) REVERT: G 354 GLU cc_start: 0.7973 (pp20) cc_final: 0.7752 (pp20) outliers start: 40 outliers final: 20 residues processed: 276 average time/residue: 0.2436 time to fit residues: 106.3120 Evaluate side-chains 259 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 238 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 356 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16940 Z= 0.298 Angle : 0.642 8.125 23142 Z= 0.330 Chirality : 0.042 0.191 2793 Planarity : 0.004 0.027 2793 Dihedral : 5.259 28.395 2240 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.22 % Allowed : 16.06 % Favored : 80.71 % 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: -0.29 (0.20), residues: 2037 helix: 1.61 (0.15), residues: 1288 sheet: -0.22 (0.54), residues: 84 loop : -4.12 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 104 HIS 0.002 0.001 HIS B 106 PHE 0.013 0.001 PHE D 126 TYR 0.018 0.002 TYR F 327 ARG 0.003 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 240 time to evaluate : 1.983 Fit side-chains revert: symmetry clash REVERT: A 54 PHE cc_start: 0.7907 (m-80) cc_final: 0.6553 (t80) REVERT: A 244 ASP cc_start: 0.6838 (OUTLIER) cc_final: 0.6225 (p0) REVERT: A 354 GLU cc_start: 0.8045 (pp20) cc_final: 0.7514 (pt0) REVERT: B 54 PHE cc_start: 0.8105 (m-80) cc_final: 0.7822 (m-80) REVERT: B 104 TRP cc_start: 0.7829 (p-90) cc_final: 0.7580 (p-90) REVERT: C 104 TRP cc_start: 0.7959 (p-90) cc_final: 0.7587 (p-90) REVERT: C 244 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6783 (p0) REVERT: D 244 ASP cc_start: 0.6806 (p0) cc_final: 0.6475 (p0) REVERT: D 312 GLU cc_start: 0.7756 (pt0) cc_final: 0.7468 (pt0) REVERT: E 51 SER cc_start: 0.8594 (m) cc_final: 0.8383 (m) REVERT: E 327 TYR cc_start: 0.8619 (m-80) cc_final: 0.8209 (m-80) REVERT: F 54 PHE cc_start: 0.8085 (m-80) cc_final: 0.7797 (m-80) REVERT: F 63 GLN cc_start: 0.8080 (mm110) cc_final: 0.7879 (mm-40) REVERT: F 244 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.7125 (p0) REVERT: G 54 PHE cc_start: 0.8149 (m-80) cc_final: 0.6759 (t80) REVERT: G 63 GLN cc_start: 0.8075 (mm110) cc_final: 0.7690 (mm-40) REVERT: G 312 GLU cc_start: 0.7833 (pt0) cc_final: 0.7441 (pt0) outliers start: 58 outliers final: 47 residues processed: 277 average time/residue: 0.2523 time to fit residues: 109.9460 Evaluate side-chains 275 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 225 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 235 TYR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 356 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN C 63 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 266 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16940 Z= 0.263 Angle : 0.620 6.983 23142 Z= 0.320 Chirality : 0.041 0.207 2793 Planarity : 0.004 0.027 2793 Dihedral : 5.185 27.832 2240 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 3.61 % Allowed : 17.84 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 2037 helix: 1.78 (0.15), residues: 1295 sheet: -0.29 (0.52), residues: 84 loop : -3.98 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 104 HIS 0.002 0.001 HIS B 106 PHE 0.012 0.001 PHE D 126 TYR 0.015 0.001 TYR F 25 ARG 0.002 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 240 time to evaluate : 2.083 Fit side-chains revert: symmetry clash REVERT: A 54 PHE cc_start: 0.7912 (m-80) cc_final: 0.6551 (t80) REVERT: A 244 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6288 (p0) REVERT: A 354 GLU cc_start: 0.7991 (pp20) cc_final: 0.7593 (pt0) REVERT: B 54 PHE cc_start: 0.8109 (m-80) cc_final: 0.7817 (m-80) REVERT: B 104 TRP cc_start: 0.7826 (p-90) cc_final: 0.7583 (p-90) REVERT: B 354 GLU cc_start: 0.7859 (pp20) cc_final: 0.7655 (pp20) REVERT: C 104 TRP cc_start: 0.7921 (p-90) cc_final: 0.7545 (p-90) REVERT: C 244 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6742 (p0) REVERT: D 104 TRP cc_start: 0.7827 (p-90) cc_final: 0.7513 (p-90) REVERT: D 244 ASP cc_start: 0.6879 (OUTLIER) cc_final: 0.6536 (p0) REVERT: D 312 GLU cc_start: 0.7731 (pt0) cc_final: 0.7445 (pt0) REVERT: E 51 SER cc_start: 0.8621 (m) cc_final: 0.8419 (m) REVERT: E 327 TYR cc_start: 0.8585 (m-80) cc_final: 0.8110 (m-80) REVERT: F 54 PHE cc_start: 0.8089 (m-80) cc_final: 0.7774 (m-80) REVERT: F 244 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.7024 (p0) REVERT: G 51 SER cc_start: 0.8636 (m) cc_final: 0.8422 (m) REVERT: G 54 PHE cc_start: 0.8168 (m-80) cc_final: 0.6775 (t80) REVERT: G 63 GLN cc_start: 0.8074 (mm110) cc_final: 0.7655 (mm-40) REVERT: G 312 GLU cc_start: 0.7787 (pt0) cc_final: 0.7397 (pt0) outliers start: 65 outliers final: 59 residues processed: 285 average time/residue: 0.2492 time to fit residues: 112.0115 Evaluate side-chains 290 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 227 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 235 TYR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 356 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 0.3980 chunk 111 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16940 Z= 0.268 Angle : 0.621 6.424 23142 Z= 0.320 Chirality : 0.041 0.212 2793 Planarity : 0.004 0.029 2793 Dihedral : 5.144 27.734 2240 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.22 % Allowed : 18.34 % Favored : 77.43 % 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: 0.07 (0.20), residues: 2037 helix: 1.85 (0.15), residues: 1295 sheet: -0.30 (0.51), residues: 84 loop : -3.91 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 104 HIS 0.002 0.001 HIS E 330 PHE 0.012 0.001 PHE E 126 TYR 0.016 0.001 TYR D 25 ARG 0.002 0.000 ARG F 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 239 time to evaluate : 1.891 Fit side-chains revert: symmetry clash REVERT: A 54 PHE cc_start: 0.7918 (m-80) cc_final: 0.6551 (t80) REVERT: A 244 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.6277 (p0) REVERT: A 354 GLU cc_start: 0.7997 (pp20) cc_final: 0.7613 (pt0) REVERT: B 54 PHE cc_start: 0.8126 (m-80) cc_final: 0.7864 (m-80) REVERT: B 104 TRP cc_start: 0.7824 (p-90) cc_final: 0.7576 (p-90) REVERT: C 104 TRP cc_start: 0.7943 (p-90) cc_final: 0.7581 (p-90) REVERT: C 244 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6741 (p0) REVERT: D 104 TRP cc_start: 0.7821 (p-90) cc_final: 0.7510 (p-90) REVERT: D 244 ASP cc_start: 0.6884 (OUTLIER) cc_final: 0.6533 (p0) REVERT: E 327 TYR cc_start: 0.8587 (m-80) cc_final: 0.8116 (m-80) REVERT: F 54 PHE cc_start: 0.8096 (m-80) cc_final: 0.7764 (m-80) REVERT: F 63 GLN cc_start: 0.8027 (mm110) cc_final: 0.7752 (mm-40) REVERT: F 244 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.7017 (p0) REVERT: G 51 SER cc_start: 0.8638 (m) cc_final: 0.8430 (m) REVERT: G 54 PHE cc_start: 0.8165 (m-80) cc_final: 0.6772 (t80) REVERT: G 63 GLN cc_start: 0.8075 (mm110) cc_final: 0.7630 (mm-40) REVERT: G 104 TRP cc_start: 0.7901 (p-90) cc_final: 0.7644 (p-90) REVERT: G 312 GLU cc_start: 0.7781 (pt0) cc_final: 0.7407 (pt0) outliers start: 76 outliers final: 67 residues processed: 293 average time/residue: 0.2471 time to fit residues: 113.8238 Evaluate side-chains 301 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 230 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 235 TYR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 354 GLU Chi-restraints excluded: chain G residue 356 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 0.8980 chunk 176 optimal weight: 0.4980 chunk 38 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16940 Z= 0.203 Angle : 0.593 7.516 23142 Z= 0.305 Chirality : 0.041 0.212 2793 Planarity : 0.004 0.030 2793 Dihedral : 4.966 26.150 2240 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.78 % Allowed : 20.01 % Favored : 76.21 % 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: 0.28 (0.21), residues: 2037 helix: 1.98 (0.15), residues: 1302 sheet: -0.37 (0.50), residues: 84 loop : -3.78 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.002 0.001 HIS E 330 PHE 0.009 0.001 PHE E 126 TYR 0.015 0.001 TYR C 327 ARG 0.002 0.000 ARG F 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 243 time to evaluate : 1.929 Fit side-chains REVERT: A 54 PHE cc_start: 0.7922 (m-80) cc_final: 0.6536 (t80) REVERT: A 244 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6347 (p0) REVERT: A 354 GLU cc_start: 0.7998 (pp20) cc_final: 0.7600 (pt0) REVERT: B 54 PHE cc_start: 0.8060 (m-80) cc_final: 0.7759 (m-80) REVERT: B 104 TRP cc_start: 0.7783 (p-90) cc_final: 0.7564 (p-90) REVERT: C 104 TRP cc_start: 0.7904 (p-90) cc_final: 0.7559 (p-90) REVERT: C 244 ASP cc_start: 0.6858 (OUTLIER) cc_final: 0.6604 (p0) REVERT: D 104 TRP cc_start: 0.7782 (p-90) cc_final: 0.7516 (p-90) REVERT: D 244 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6487 (p0) REVERT: D 266 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: E 327 TYR cc_start: 0.8552 (m-80) cc_final: 0.8129 (m-80) REVERT: F 54 PHE cc_start: 0.8068 (m-80) cc_final: 0.7713 (m-80) REVERT: F 244 ASP cc_start: 0.7264 (p0) cc_final: 0.7017 (p0) REVERT: F 354 GLU cc_start: 0.7912 (pp20) cc_final: 0.7589 (pt0) REVERT: G 54 PHE cc_start: 0.8148 (m-80) cc_final: 0.6763 (t80) REVERT: G 63 GLN cc_start: 0.8052 (mm110) cc_final: 0.7587 (mm-40) REVERT: G 312 GLU cc_start: 0.7744 (pt0) cc_final: 0.7460 (pt0) outliers start: 68 outliers final: 58 residues processed: 292 average time/residue: 0.2481 time to fit residues: 115.1712 Evaluate side-chains 300 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 238 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 235 TYR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 354 GLU Chi-restraints excluded: chain G residue 356 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 165 optimal weight: 0.2980 chunk 109 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16940 Z= 0.219 Angle : 0.595 7.192 23142 Z= 0.307 Chirality : 0.041 0.216 2793 Planarity : 0.004 0.031 2793 Dihedral : 4.885 26.096 2240 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.84 % Allowed : 20.68 % Favored : 75.49 % 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: 0.38 (0.21), residues: 2037 helix: 2.08 (0.15), residues: 1295 sheet: -0.34 (0.49), residues: 84 loop : -3.73 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 104 HIS 0.002 0.001 HIS E 330 PHE 0.010 0.001 PHE E 126 TYR 0.014 0.001 TYR G 327 ARG 0.002 0.000 ARG F 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 246 time to evaluate : 1.898 Fit side-chains revert: symmetry clash REVERT: A 54 PHE cc_start: 0.7928 (m-80) cc_final: 0.6537 (t80) REVERT: A 244 ASP cc_start: 0.6959 (OUTLIER) cc_final: 0.6372 (p0) REVERT: A 354 GLU cc_start: 0.8004 (pp20) cc_final: 0.7642 (pt0) REVERT: B 54 PHE cc_start: 0.8059 (m-80) cc_final: 0.7756 (m-80) REVERT: C 104 TRP cc_start: 0.7896 (p-90) cc_final: 0.7537 (p-90) REVERT: C 244 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.6632 (p0) REVERT: D 104 TRP cc_start: 0.7781 (p-90) cc_final: 0.7503 (p-90) REVERT: D 244 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.6471 (p0) REVERT: E 327 TYR cc_start: 0.8557 (m-80) cc_final: 0.8138 (m-80) REVERT: F 244 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6742 (p0) REVERT: F 354 GLU cc_start: 0.7958 (pp20) cc_final: 0.7651 (pt0) REVERT: G 54 PHE cc_start: 0.8134 (m-80) cc_final: 0.6740 (t80) REVERT: G 63 GLN cc_start: 0.8052 (mm110) cc_final: 0.7572 (mm-40) REVERT: G 104 TRP cc_start: 0.7871 (p-90) cc_final: 0.7652 (p-90) REVERT: G 312 GLU cc_start: 0.7696 (pt0) cc_final: 0.7448 (pt0) outliers start: 69 outliers final: 60 residues processed: 297 average time/residue: 0.2495 time to fit residues: 117.3271 Evaluate side-chains 304 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 240 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 235 TYR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 356 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.0670 chunk 116 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 HIS G 282 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16940 Z= 0.409 Angle : 0.706 7.291 23142 Z= 0.364 Chirality : 0.045 0.227 2793 Planarity : 0.004 0.035 2793 Dihedral : 5.262 28.587 2240 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.50 % Allowed : 20.51 % Favored : 74.99 % 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: 0.08 (0.20), residues: 2037 helix: 1.82 (0.15), residues: 1288 sheet: -0.02 (0.52), residues: 84 loop : -3.77 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 104 HIS 0.002 0.001 HIS B 106 PHE 0.018 0.002 PHE E 126 TYR 0.021 0.002 TYR B 25 ARG 0.003 0.000 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 246 time to evaluate : 2.118 Fit side-chains revert: symmetry clash REVERT: A 54 PHE cc_start: 0.7965 (m-80) cc_final: 0.6558 (t80) REVERT: A 244 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6582 (p0) REVERT: A 354 GLU cc_start: 0.8040 (pp20) cc_final: 0.7699 (pt0) REVERT: B 54 PHE cc_start: 0.8120 (m-80) cc_final: 0.7839 (m-80) REVERT: C 104 TRP cc_start: 0.7985 (p-90) cc_final: 0.7638 (p-90) REVERT: C 244 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6803 (p0) REVERT: D 244 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6595 (p0) REVERT: E 327 TYR cc_start: 0.8666 (m-80) cc_final: 0.8222 (m-80) REVERT: E 329 ASP cc_start: 0.8329 (m-30) cc_final: 0.8120 (m-30) REVERT: F 244 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6961 (p0) REVERT: F 354 GLU cc_start: 0.8023 (pp20) cc_final: 0.7712 (pt0) REVERT: G 54 PHE cc_start: 0.8111 (m-80) cc_final: 0.6749 (t80) REVERT: G 63 GLN cc_start: 0.8058 (mm110) cc_final: 0.7566 (mm-40) REVERT: G 312 GLU cc_start: 0.7780 (pt0) cc_final: 0.7518 (pt0) outliers start: 81 outliers final: 72 residues processed: 306 average time/residue: 0.2555 time to fit residues: 122.3207 Evaluate side-chains 312 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 236 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 235 TYR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 356 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 164 optimal weight: 0.0870 chunk 172 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 ASN G 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16940 Z= 0.192 Angle : 0.599 6.700 23142 Z= 0.309 Chirality : 0.041 0.215 2793 Planarity : 0.004 0.033 2793 Dihedral : 4.916 25.494 2240 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.22 % Allowed : 21.68 % Favored : 75.10 % 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: 0.37 (0.20), residues: 2037 helix: 2.11 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -3.51 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 74 HIS 0.002 0.001 HIS C 106 PHE 0.009 0.001 PHE A 83 TYR 0.014 0.001 TYR B 111 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 247 time to evaluate : 2.032 Fit side-chains revert: symmetry clash REVERT: A 54 PHE cc_start: 0.7889 (m-80) cc_final: 0.6586 (t80) REVERT: A 244 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6414 (p0) REVERT: A 354 GLU cc_start: 0.8002 (pp20) cc_final: 0.7657 (pt0) REVERT: B 54 PHE cc_start: 0.8041 (m-80) cc_final: 0.7737 (m-80) REVERT: C 104 TRP cc_start: 0.7828 (p-90) cc_final: 0.7501 (p-90) REVERT: C 244 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6755 (p0) REVERT: D 104 TRP cc_start: 0.7757 (p-90) cc_final: 0.7530 (p-90) REVERT: E 327 TYR cc_start: 0.8523 (m-80) cc_final: 0.8129 (m-80) REVERT: F 244 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6817 (p0) REVERT: G 54 PHE cc_start: 0.8129 (m-80) cc_final: 0.6752 (t80) REVERT: G 104 TRP cc_start: 0.7826 (p-90) cc_final: 0.7611 (p-90) REVERT: G 312 GLU cc_start: 0.7641 (pt0) cc_final: 0.7407 (pt0) outliers start: 58 outliers final: 52 residues processed: 290 average time/residue: 0.2499 time to fit residues: 113.9009 Evaluate side-chains 298 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 243 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 235 TYR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 354 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16940 Z= 0.206 Angle : 0.601 6.994 23142 Z= 0.311 Chirality : 0.041 0.224 2793 Planarity : 0.004 0.035 2793 Dihedral : 4.796 25.456 2240 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.06 % Allowed : 21.85 % Favored : 75.10 % 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: 0.46 (0.21), residues: 2037 helix: 2.21 (0.15), residues: 1295 sheet: None (None), residues: 0 loop : -3.48 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.002 0.001 HIS F 330 PHE 0.009 0.001 PHE E 83 TYR 0.013 0.001 TYR B 111 ARG 0.002 0.000 ARG F 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 241 time to evaluate : 2.083 Fit side-chains revert: symmetry clash REVERT: A 54 PHE cc_start: 0.7946 (m-80) cc_final: 0.6641 (t80) REVERT: A 244 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6396 (p0) REVERT: A 354 GLU cc_start: 0.8005 (pp20) cc_final: 0.7659 (pt0) REVERT: B 54 PHE cc_start: 0.8034 (m-80) cc_final: 0.7709 (m-80) REVERT: C 104 TRP cc_start: 0.7868 (p-90) cc_final: 0.7570 (p-90) REVERT: C 244 ASP cc_start: 0.6966 (p0) cc_final: 0.6723 (p0) REVERT: D 63 GLN cc_start: 0.7970 (tp40) cc_final: 0.7516 (tp40) REVERT: D 104 TRP cc_start: 0.7783 (p-90) cc_final: 0.7540 (p-90) REVERT: D 245 GLU cc_start: 0.7086 (pt0) cc_final: 0.6609 (pt0) REVERT: F 244 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6775 (p0) REVERT: F 354 GLU cc_start: 0.7948 (pp20) cc_final: 0.7672 (pt0) REVERT: G 54 PHE cc_start: 0.8131 (m-80) cc_final: 0.6726 (t80) REVERT: G 104 TRP cc_start: 0.7865 (p-90) cc_final: 0.7649 (p-90) REVERT: G 312 GLU cc_start: 0.7608 (pt0) cc_final: 0.7366 (pt0) outliers start: 55 outliers final: 50 residues processed: 286 average time/residue: 0.2590 time to fit residues: 115.1487 Evaluate side-chains 290 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 238 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 235 TYR Chi-restraints excluded: chain G residue 238 SER Chi-restraints excluded: chain G residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099387 restraints weight = 27432.238| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.42 r_work: 0.3093 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16940 Z= 0.286 Angle : 0.639 7.058 23142 Z= 0.331 Chirality : 0.043 0.225 2793 Planarity : 0.004 0.036 2793 Dihedral : 4.953 26.328 2240 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.45 % Allowed : 21.29 % Favored : 75.26 % 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: 0.37 (0.20), residues: 2037 helix: 2.09 (0.15), residues: 1295 sheet: 0.55 (0.75), residues: 42 loop : -3.66 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 104 HIS 0.002 0.001 HIS E 330 PHE 0.013 0.001 PHE E 126 TYR 0.017 0.001 TYR B 25 ARG 0.003 0.000 ARG D 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3090.79 seconds wall clock time: 57 minutes 25.70 seconds (3445.70 seconds total)