Starting phenix.real_space_refine on Sat Jan 20 18:13:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f74_28894/01_2024/8f74_28894_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f74_28894/01_2024/8f74_28894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f74_28894/01_2024/8f74_28894.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f74_28894/01_2024/8f74_28894.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f74_28894/01_2024/8f74_28894_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f74_28894/01_2024/8f74_28894_updated.pdb" } resolution = 3.1 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= 0.003 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 106 5.16 5 C 10580 2.51 5 N 2524 2.21 5 O 2794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 29": "OD1" <-> "OD2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A ASP 165": "OD1" <-> "OD2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B ASP 380": "OD1" <-> "OD2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 367": "OD1" <-> "OD2" Residue "E PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ASP 104": "OD1" <-> "OD2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "F PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 296": "OD1" <-> "OD2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 352": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 16008 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2672 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "B" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2668 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Chain: "C" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2560 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain breaks: 2 Chain: "D" Number of atoms: 2637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2637 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 9, 'TRANS': 304} Chain breaks: 2 Chain: "E" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2652 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "F" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2569 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 7, 'TRANS': 301} Chain breaks: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.54, per 1000 atoms: 0.53 Number of scatterers: 16008 At special positions: 0 Unit cell: (97.464, 108.992, 134.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 4 15.00 O 2794 8.00 N 2524 7.00 C 10580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " 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: 6.53 Conformation dependent library (CDL) restraints added in 2.5 seconds 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 6 sheets defined 69.3% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 removed outlier: 4.098A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 49 Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 120 through 140 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 142 through 145 No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 147 through 164 removed outlier: 4.141A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 234 through 254 Processing helix chain 'A' and resid 259 through 284 removed outlier: 3.972A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 313 through 345 removed outlier: 4.293A pdb=" N THR A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG A 345 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 370 through 382 Processing helix chain 'A' and resid 384 through 394 removed outlier: 4.202A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'B' and resid 16 through 20 removed outlier: 4.149A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 49 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 120 through 145 Proline residue: B 126 - end of helix removed outlier: 4.604A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 165 Processing helix chain 'B' and resid 167 through 174 removed outlier: 3.537A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 254 Processing helix chain 'B' and resid 259 through 288 removed outlier: 5.051A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASN B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 342 Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 370 through 382 Processing helix chain 'B' and resid 384 through 393 removed outlier: 4.381A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 409 Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 23 through 49 removed outlier: 3.603A pdb=" N MET C 37 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 116 Processing helix chain 'C' and resid 120 through 145 Proline residue: C 126 - end of helix removed outlier: 4.657A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 164 Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 236 through 254 Processing helix chain 'C' and resid 259 through 288 removed outlier: 4.895A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASN C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 343 removed outlier: 4.272A pdb=" N THR C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU C 317 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 370 through 382 Processing helix chain 'C' and resid 384 through 390 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'D' and resid 16 through 20 removed outlier: 4.282A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 48 Processing helix chain 'D' and resid 103 through 116 Processing helix chain 'D' and resid 120 through 143 Proline residue: D 126 - end of helix removed outlier: 4.842A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 164 Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 234 through 255 Processing helix chain 'D' and resid 259 through 288 removed outlier: 4.929A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASN D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 345 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 371 through 382 Processing helix chain 'D' and resid 384 through 393 removed outlier: 4.016A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 407 Processing helix chain 'E' and resid 18 through 20 No H-bonds generated for 'chain 'E' and resid 18 through 20' Processing helix chain 'E' and resid 23 through 49 Processing helix chain 'E' and resid 103 through 116 Processing helix chain 'E' and resid 120 through 145 Proline residue: E 126 - end of helix removed outlier: 4.643A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 165 removed outlier: 4.163A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 234 through 254 Processing helix chain 'E' and resid 259 through 288 removed outlier: 5.125A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASN E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 344 removed outlier: 3.553A pdb=" N LEU E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 370 through 382 Processing helix chain 'E' and resid 384 through 393 removed outlier: 3.964A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 408 Processing helix chain 'F' and resid 23 through 48 Processing helix chain 'F' and resid 105 through 118 removed outlier: 3.525A pdb=" N ARG F 118 " --> pdb=" O MET F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 142 Proline residue: F 128 - end of helix Processing helix chain 'F' and resid 144 through 147 No H-bonds generated for 'chain 'F' and resid 144 through 147' Processing helix chain 'F' and resid 149 through 167 Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 233 through 252 Processing helix chain 'F' and resid 258 through 283 Processing helix chain 'F' and resid 298 through 301 No H-bonds generated for 'chain 'F' and resid 298 through 301' Processing helix chain 'F' and resid 313 through 343 Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 369 through 388 Proline residue: F 382 - end of helix removed outlier: 4.016A pdb=" N SER F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 407 Processing sheet with id= A, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= B, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.557A pdb=" N ILE B 53 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 52 through 56 Processing sheet with id= D, first strand: chain 'D' and resid 53 through 56 Processing sheet with id= E, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.749A pdb=" N ILE E 53 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 52 through 56 975 hydrogen bonds defined for protein. 2748 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: 4.37 Time building geometry restraints manager: 7.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2602 1.32 - 1.45: 4684 1.45 - 1.57: 8982 1.57 - 1.69: 6 1.69 - 1.81: 155 Bond restraints: 16429 Sorted by residual: bond pdb=" C10 PEE D 901 " pdb=" O4 PEE D 901 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C10 PEE B 903 " pdb=" O4 PEE B 903 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" O4P PEE A 901 " pdb=" P PEE A 901 " ideal model delta sigma weight residual 1.653 1.779 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" O4P PEE C 901 " pdb=" P PEE C 901 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" O4P PEE B 901 " pdb=" P PEE B 901 " ideal model delta sigma weight residual 1.653 1.775 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 16424 not shown) Histogram of bond angle deviations from ideal: 90.79 - 99.47: 4 99.47 - 108.16: 606 108.16 - 116.85: 10274 116.85 - 125.54: 10989 125.54 - 134.23: 293 Bond angle restraints: 22166 Sorted by residual: angle pdb=" O1P PEE C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.24 -13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.22 -13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE B 901 " pdb=" P PEE B 901 " pdb=" O2P PEE B 901 " ideal model delta sigma weight residual 119.43 133.13 -13.70 3.00e+00 1.11e-01 2.09e+01 angle pdb=" C11 PEE B 903 " pdb=" C10 PEE B 903 " pdb=" O2 PEE B 903 " ideal model delta sigma weight residual 111.70 124.70 -13.00 3.00e+00 1.11e-01 1.88e+01 angle pdb=" C11 PEE D 901 " pdb=" C10 PEE D 901 " pdb=" O2 PEE D 901 " ideal model delta sigma weight residual 111.70 124.60 -12.90 3.00e+00 1.11e-01 1.85e+01 ... (remaining 22161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 9403 34.77 - 69.54: 305 69.54 - 104.31: 23 104.31 - 139.08: 2 139.08 - 173.86: 5 Dihedral angle restraints: 9738 sinusoidal: 4086 harmonic: 5652 Sorted by residual: dihedral pdb=" CB CYS C 113 " pdb=" SG CYS C 113 " pdb=" SG CYS C 295 " pdb=" CB CYS C 295 " ideal model delta sinusoidal sigma weight residual 93.00 43.52 49.48 1 1.00e+01 1.00e-02 3.36e+01 dihedral pdb=" N PEE C 901 " pdb=" C4 PEE C 901 " pdb=" C5 PEE C 901 " pdb=" O4P PEE C 901 " ideal model delta sinusoidal sigma weight residual 303.03 129.17 173.86 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 PEE C 901 " pdb=" C1 PEE C 901 " pdb=" C2 PEE C 901 " pdb=" O3P PEE C 901 " ideal model delta sinusoidal sigma weight residual -59.96 111.18 -171.14 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 9735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2000 0.056 - 0.112: 374 0.112 - 0.168: 20 0.168 - 0.224: 2 0.224 - 0.280: 3 Chirality restraints: 2399 Sorted by residual: chirality pdb=" CB VAL E 283 " pdb=" CA VAL E 283 " pdb=" CG1 VAL E 283 " pdb=" CG2 VAL E 283 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C2 PEE F 901 " pdb=" C1 PEE F 901 " pdb=" C3 PEE F 901 " pdb=" O2 PEE F 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.61 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB THR B 44 " pdb=" CA THR B 44 " pdb=" OG1 THR B 44 " pdb=" CG2 THR B 44 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2396 not shown) Planarity restraints: 2678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 23 " -0.021 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP F 23 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP F 23 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP F 23 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 23 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 23 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 23 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 23 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 168 " -0.017 2.00e-02 2.50e+03 1.67e-02 6.94e+00 pdb=" CG TRP C 168 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 168 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 168 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 168 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 168 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 168 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 168 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 155 " -0.020 2.00e-02 2.50e+03 2.05e-02 6.33e+00 pdb=" CG HIS D 155 " 0.044 2.00e-02 2.50e+03 pdb=" ND1 HIS D 155 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS D 155 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS D 155 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS D 155 " -0.003 2.00e-02 2.50e+03 ... (remaining 2675 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1381 2.74 - 3.28: 16118 3.28 - 3.82: 28547 3.82 - 4.36: 32414 4.36 - 4.90: 56338 Nonbonded interactions: 134798 Sorted by model distance: nonbonded pdb=" NE2 GLN A 46 " pdb=" O LYS A 123 " model vdw 2.206 2.520 nonbonded pdb=" OH TYR B 351 " pdb=" OD2 ASP B 380 " model vdw 2.249 2.440 nonbonded pdb=" OG1 THR E 303 " pdb=" OH TYR E 308 " model vdw 2.269 2.440 nonbonded pdb=" O PRO D 167 " pdb=" OG1 THR D 170 " model vdw 2.272 2.440 nonbonded pdb=" O ILE E 278 " pdb=" OG1 THR E 282 " model vdw 2.273 2.440 ... (remaining 134793 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 68 or resid 93 through 175 or resid 235 through \ 402 or (resid 903 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name O2 or name O4 )))) selection = (chain 'B' and (resid 15 through 68 or resid 93 through 175 or resid 235 through \ 402 or (resid 903 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name O2 or name O4 )))) selection = (chain 'C' and (resid 15 through 402 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name O2 or name O4 ) \ ))) selection = (chain 'D' and (resid 15 through 175 or resid 235 through 402 or resid 902)) selection = (chain 'E' and (resid 15 through 175 or resid 235 through 402 or resid 903)) } 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: 3.940 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: 15.730 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 43.600 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.060 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.005 0.150 16429 Z= 0.329 Angle : 0.723 13.805 22166 Z= 0.389 Chirality : 0.041 0.280 2399 Planarity : 0.005 0.046 2678 Dihedral : 17.290 173.856 6027 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.06 % Allowed : 18.43 % Favored : 81.51 % 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: 0.91 (0.19), residues: 1845 helix: 1.23 (0.13), residues: 1289 sheet: -0.28 (0.51), residues: 107 loop : -0.85 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP F 23 HIS 0.021 0.001 HIS D 155 PHE 0.034 0.002 PHE C 142 TYR 0.030 0.002 TYR E 281 ARG 0.009 0.001 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 1.922 Fit side-chains revert: symmetry clash REVERT: A 388 LYS cc_start: 0.8103 (tttt) cc_final: 0.7687 (tmtt) REVERT: C 337 MET cc_start: 0.6264 (tmm) cc_final: 0.6021 (tmm) REVERT: D 249 LYS cc_start: 0.8530 (ptmt) cc_final: 0.8269 (ptmm) REVERT: D 399 GLU cc_start: 0.6297 (mt-10) cc_final: 0.5806 (tp30) REVERT: E 30 TYR cc_start: 0.7565 (m-10) cc_final: 0.7358 (m-10) REVERT: E 99 TYR cc_start: 0.8508 (m-80) cc_final: 0.8268 (m-80) REVERT: F 144 PHE cc_start: 0.5912 (t80) cc_final: 0.5565 (t80) outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.2745 time to fit residues: 105.7934 Evaluate side-chains 216 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 144 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS B 239 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN E 408 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16429 Z= 0.348 Angle : 0.530 10.510 22166 Z= 0.288 Chirality : 0.040 0.149 2399 Planarity : 0.004 0.037 2678 Dihedral : 9.336 157.998 2256 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.21 % Allowed : 16.83 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 1845 helix: 1.59 (0.14), residues: 1294 sheet: -0.30 (0.51), residues: 106 loop : -0.74 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 23 HIS 0.012 0.002 HIS A 253 PHE 0.026 0.002 PHE E 324 TYR 0.018 0.002 TYR F 330 ARG 0.004 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 228 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7816 (tp30) cc_final: 0.7363 (tp30) REVERT: B 168 TRP cc_start: 0.8026 (t-100) cc_final: 0.7803 (t-100) REVERT: C 37 MET cc_start: 0.8352 (mtt) cc_final: 0.7260 (tmm) REVERT: C 308 TYR cc_start: 0.9079 (m-80) cc_final: 0.8621 (m-80) REVERT: C 337 MET cc_start: 0.6299 (tmm) cc_final: 0.6053 (tmm) REVERT: E 250 PHE cc_start: 0.6535 (t80) cc_final: 0.6220 (t80) REVERT: F 143 ASN cc_start: 0.5343 (OUTLIER) cc_final: 0.4630 (p0) REVERT: F 279 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.8082 (p90) outliers start: 56 outliers final: 31 residues processed: 265 average time/residue: 0.2700 time to fit residues: 109.4468 Evaluate side-chains 243 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 210 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 113 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 180 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN D 287 HIS E 155 HIS E 287 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16429 Z= 0.237 Angle : 0.461 8.690 22166 Z= 0.251 Chirality : 0.038 0.187 2399 Planarity : 0.003 0.034 2678 Dihedral : 8.073 155.419 2256 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.55 % Allowed : 17.12 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.19), residues: 1845 helix: 1.63 (0.14), residues: 1306 sheet: -0.19 (0.51), residues: 107 loop : -0.69 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 23 HIS 0.006 0.001 HIS E 253 PHE 0.019 0.001 PHE E 324 TYR 0.017 0.001 TYR E 351 ARG 0.003 0.000 ARG F 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 236 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7793 (tp30) cc_final: 0.7314 (tp30) REVERT: B 168 TRP cc_start: 0.8060 (t-100) cc_final: 0.7557 (t-100) REVERT: B 245 GLU cc_start: 0.7913 (tp30) cc_final: 0.7445 (tp30) REVERT: B 404 GLN cc_start: 0.8065 (pp30) cc_final: 0.7726 (pp30) REVERT: C 37 MET cc_start: 0.8354 (mtt) cc_final: 0.7221 (tmm) REVERT: C 308 TYR cc_start: 0.9066 (m-80) cc_final: 0.8516 (m-80) REVERT: C 375 MET cc_start: 0.6819 (mtm) cc_final: 0.6581 (mtm) REVERT: D 375 MET cc_start: 0.7619 (mtt) cc_final: 0.7364 (mtm) REVERT: E 250 PHE cc_start: 0.6563 (t80) cc_final: 0.6007 (t80) REVERT: F 279 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8139 (p90) outliers start: 62 outliers final: 41 residues processed: 271 average time/residue: 0.2619 time to fit residues: 108.0320 Evaluate side-chains 259 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 217 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 391 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 167 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 87 optimal weight: 0.2980 chunk 159 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS E 155 HIS E 287 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16429 Z= 0.181 Angle : 0.437 7.116 22166 Z= 0.239 Chirality : 0.037 0.190 2399 Planarity : 0.003 0.031 2678 Dihedral : 7.384 151.917 2256 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.66 % Allowed : 17.12 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.20), residues: 1845 helix: 1.77 (0.14), residues: 1300 sheet: -0.04 (0.51), residues: 107 loop : -0.56 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 23 HIS 0.010 0.001 HIS D 155 PHE 0.018 0.001 PHE A 250 TYR 0.017 0.001 TYR E 351 ARG 0.005 0.000 ARG E 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 233 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8278 (mp) REVERT: A 154 GLU cc_start: 0.7778 (tp30) cc_final: 0.7285 (tp30) REVERT: A 239 GLN cc_start: 0.7552 (mm110) cc_final: 0.7323 (mm110) REVERT: A 332 TYR cc_start: 0.8634 (t80) cc_final: 0.8394 (t80) REVERT: B 168 TRP cc_start: 0.8060 (t-100) cc_final: 0.7534 (t-100) REVERT: B 245 GLU cc_start: 0.7880 (tp30) cc_final: 0.7410 (tp30) REVERT: B 404 GLN cc_start: 0.8005 (pp30) cc_final: 0.7662 (pp30) REVERT: C 37 MET cc_start: 0.8304 (mtt) cc_final: 0.7130 (tmm) REVERT: C 308 TYR cc_start: 0.9068 (m-80) cc_final: 0.8466 (m-80) REVERT: C 337 MET cc_start: 0.6195 (tmm) cc_final: 0.5972 (tmm) REVERT: D 155 HIS cc_start: 0.7001 (t-170) cc_final: 0.6733 (t-170) REVERT: D 275 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.8009 (t80) REVERT: D 375 MET cc_start: 0.7580 (mtt) cc_final: 0.7324 (mtm) REVERT: D 382 TYR cc_start: 0.8582 (t80) cc_final: 0.8355 (t80) REVERT: E 389 ARG cc_start: 0.6288 (ptm-80) cc_final: 0.6010 (ptm-80) REVERT: F 143 ASN cc_start: 0.5265 (OUTLIER) cc_final: 0.4539 (p0) REVERT: F 279 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.8018 (p90) outliers start: 64 outliers final: 40 residues processed: 275 average time/residue: 0.2613 time to fit residues: 109.3095 Evaluate side-chains 263 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 219 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 385 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 5.9990 chunk 100 optimal weight: 0.0470 chunk 2 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN D 287 HIS E 155 HIS E 287 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16429 Z= 0.185 Angle : 0.436 6.207 22166 Z= 0.239 Chirality : 0.037 0.184 2399 Planarity : 0.003 0.030 2678 Dihedral : 7.074 149.573 2256 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.01 % Allowed : 17.63 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.20), residues: 1845 helix: 1.83 (0.14), residues: 1299 sheet: -0.01 (0.51), residues: 107 loop : -0.53 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 23 HIS 0.007 0.001 HIS E 155 PHE 0.020 0.001 PHE A 250 TYR 0.014 0.001 TYR E 351 ARG 0.003 0.000 ARG E 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 237 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8241 (mp) REVERT: A 154 GLU cc_start: 0.7761 (tp30) cc_final: 0.7248 (tp30) REVERT: A 332 TYR cc_start: 0.8637 (t80) cc_final: 0.8397 (t80) REVERT: B 168 TRP cc_start: 0.8117 (t-100) cc_final: 0.7643 (t-100) REVERT: B 245 GLU cc_start: 0.7855 (tp30) cc_final: 0.7535 (tp30) REVERT: B 404 GLN cc_start: 0.8110 (pp30) cc_final: 0.7764 (pp30) REVERT: C 37 MET cc_start: 0.8301 (mtt) cc_final: 0.7123 (tmm) REVERT: C 308 TYR cc_start: 0.9081 (m-80) cc_final: 0.8452 (m-80) REVERT: C 375 MET cc_start: 0.6833 (mtm) cc_final: 0.6507 (mtm) REVERT: D 275 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.8001 (t80) REVERT: D 382 TYR cc_start: 0.8610 (t80) cc_final: 0.8386 (t80) REVERT: F 143 ASN cc_start: 0.5158 (OUTLIER) cc_final: 0.4446 (p0) REVERT: F 157 HIS cc_start: 0.7210 (OUTLIER) cc_final: 0.6991 (t-170) REVERT: F 279 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.8005 (p90) REVERT: F 323 TYR cc_start: 0.8479 (t80) cc_final: 0.8069 (t80) REVERT: F 391 PHE cc_start: 0.5293 (m-80) cc_final: 0.4551 (m-80) outliers start: 70 outliers final: 49 residues processed: 283 average time/residue: 0.2597 time to fit residues: 111.8361 Evaluate side-chains 268 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 214 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 385 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 35 optimal weight: 0.0670 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 178 optimal weight: 0.1980 chunk 147 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN D 287 HIS E 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16429 Z= 0.164 Angle : 0.431 5.564 22166 Z= 0.235 Chirality : 0.037 0.182 2399 Planarity : 0.003 0.029 2678 Dihedral : 6.766 146.222 2256 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.61 % Allowed : 18.37 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.20), residues: 1845 helix: 1.90 (0.14), residues: 1299 sheet: 0.17 (0.51), residues: 107 loop : -0.47 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 23 HIS 0.015 0.001 HIS A 253 PHE 0.019 0.001 PHE A 250 TYR 0.016 0.001 TYR E 351 ARG 0.003 0.000 ARG E 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 239 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7746 (tp30) cc_final: 0.7216 (tp30) REVERT: A 399 GLU cc_start: 0.8336 (pt0) cc_final: 0.8131 (pt0) REVERT: B 168 TRP cc_start: 0.8083 (t-100) cc_final: 0.7558 (t-100) REVERT: B 245 GLU cc_start: 0.7826 (tp30) cc_final: 0.7510 (tp30) REVERT: B 404 GLN cc_start: 0.8142 (pp30) cc_final: 0.7805 (pp30) REVERT: C 37 MET cc_start: 0.8298 (mtt) cc_final: 0.7136 (tmm) REVERT: C 337 MET cc_start: 0.5922 (tmm) cc_final: 0.5697 (tmm) REVERT: D 155 HIS cc_start: 0.7095 (t-170) cc_final: 0.6808 (t-170) REVERT: D 249 LYS cc_start: 0.8686 (ptmt) cc_final: 0.8338 (ptmm) REVERT: D 275 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7984 (t80) REVERT: D 382 TYR cc_start: 0.8588 (t80) cc_final: 0.8378 (t80) REVERT: F 143 ASN cc_start: 0.5124 (OUTLIER) cc_final: 0.4375 (p0) REVERT: F 279 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.8008 (p90) REVERT: F 323 TYR cc_start: 0.8457 (t80) cc_final: 0.8085 (t80) REVERT: F 391 PHE cc_start: 0.5402 (m-80) cc_final: 0.4650 (m-80) outliers start: 63 outliers final: 45 residues processed: 283 average time/residue: 0.2744 time to fit residues: 117.2981 Evaluate side-chains 269 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 221 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 110 optimal weight: 0.0970 chunk 108 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS E 287 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 0.034 16429 Z= 0.171 Angle : 0.434 5.809 22166 Z= 0.236 Chirality : 0.037 0.160 2399 Planarity : 0.003 0.031 2678 Dihedral : 6.602 144.348 2256 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.32 % Allowed : 18.83 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.20), residues: 1845 helix: 1.93 (0.14), residues: 1299 sheet: 0.08 (0.50), residues: 107 loop : -0.42 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 23 HIS 0.013 0.001 HIS A 253 PHE 0.020 0.001 PHE A 250 TYR 0.022 0.001 TYR C 382 ARG 0.003 0.000 ARG E 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 227 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7752 (tp30) cc_final: 0.7218 (tp30) REVERT: A 399 GLU cc_start: 0.8411 (pt0) cc_final: 0.8208 (pt0) REVERT: B 168 TRP cc_start: 0.8088 (t-100) cc_final: 0.7559 (t-100) REVERT: B 245 GLU cc_start: 0.7844 (tp30) cc_final: 0.7493 (tp30) REVERT: B 404 GLN cc_start: 0.8152 (pp30) cc_final: 0.7813 (pp30) REVERT: C 37 MET cc_start: 0.8297 (mtt) cc_final: 0.7127 (tmm) REVERT: C 337 MET cc_start: 0.5939 (tmm) cc_final: 0.5687 (tmm) REVERT: D 249 LYS cc_start: 0.8665 (ptmt) cc_final: 0.8310 (ptmm) REVERT: D 275 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7984 (t80) REVERT: D 382 TYR cc_start: 0.8596 (t80) cc_final: 0.8370 (t80) REVERT: E 156 PHE cc_start: 0.7843 (t80) cc_final: 0.7472 (t80) REVERT: F 49 GLN cc_start: 0.6338 (tp40) cc_final: 0.6005 (tp40) REVERT: F 143 ASN cc_start: 0.5180 (OUTLIER) cc_final: 0.4447 (p0) REVERT: F 279 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.8000 (p90) REVERT: F 323 TYR cc_start: 0.8480 (t80) cc_final: 0.8138 (t80) REVERT: F 391 PHE cc_start: 0.5407 (m-80) cc_final: 0.4647 (m-80) outliers start: 58 outliers final: 42 residues processed: 267 average time/residue: 0.2604 time to fit residues: 105.9749 Evaluate side-chains 262 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.7980 chunk 70 optimal weight: 0.3980 chunk 105 optimal weight: 9.9990 chunk 53 optimal weight: 0.0770 chunk 34 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 87 optimal weight: 0.0870 chunk 16 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 404 GLN B 66 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN D 287 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16429 Z= 0.139 Angle : 0.426 8.780 22166 Z= 0.233 Chirality : 0.037 0.180 2399 Planarity : 0.003 0.031 2678 Dihedral : 6.253 138.613 2256 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.15 % Allowed : 19.12 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.20), residues: 1845 helix: 2.00 (0.14), residues: 1300 sheet: 0.06 (0.52), residues: 100 loop : -0.31 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP F 23 HIS 0.015 0.001 HIS A 253 PHE 0.021 0.001 PHE E 250 TYR 0.020 0.001 TYR C 382 ARG 0.003 0.000 ARG E 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 245 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7736 (tp30) cc_final: 0.7184 (tp30) REVERT: A 399 GLU cc_start: 0.8395 (pt0) cc_final: 0.8162 (pt0) REVERT: B 168 TRP cc_start: 0.8110 (t-100) cc_final: 0.7551 (t-100) REVERT: B 245 GLU cc_start: 0.7809 (tp30) cc_final: 0.7468 (tp30) REVERT: B 404 GLN cc_start: 0.8159 (pp30) cc_final: 0.7820 (pp30) REVERT: C 37 MET cc_start: 0.8231 (mtt) cc_final: 0.7076 (tmm) REVERT: C 102 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7198 (m-30) REVERT: C 158 SER cc_start: 0.8128 (t) cc_final: 0.7901 (p) REVERT: C 308 TYR cc_start: 0.9059 (m-80) cc_final: 0.8513 (m-80) REVERT: D 275 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7942 (t80) REVERT: D 382 TYR cc_start: 0.8592 (t80) cc_final: 0.8352 (t80) REVERT: E 156 PHE cc_start: 0.7784 (t80) cc_final: 0.7420 (t80) REVERT: E 381 GLN cc_start: 0.8025 (mm110) cc_final: 0.7812 (mm-40) REVERT: F 49 GLN cc_start: 0.6336 (tp40) cc_final: 0.6064 (tp40) REVERT: F 143 ASN cc_start: 0.5123 (OUTLIER) cc_final: 0.4456 (p0) REVERT: F 279 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7852 (p90) REVERT: F 309 ASN cc_start: 0.8837 (p0) cc_final: 0.8627 (p0) REVERT: F 323 TYR cc_start: 0.8468 (t80) cc_final: 0.8147 (t80) REVERT: F 387 ARG cc_start: 0.5276 (ttp80) cc_final: 0.4553 (ttm110) REVERT: F 391 PHE cc_start: 0.5423 (m-80) cc_final: 0.4710 (m-80) outliers start: 55 outliers final: 38 residues processed: 285 average time/residue: 0.2648 time to fit residues: 114.4228 Evaluate side-chains 268 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 226 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 366 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 253 HIS B 66 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN D 287 HIS E 287 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16429 Z= 0.203 Angle : 0.462 7.854 22166 Z= 0.251 Chirality : 0.038 0.190 2399 Planarity : 0.003 0.032 2678 Dihedral : 6.357 138.404 2256 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.15 % Allowed : 19.18 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.20), residues: 1845 helix: 1.95 (0.14), residues: 1301 sheet: -0.02 (0.52), residues: 101 loop : -0.34 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP F 23 HIS 0.014 0.001 HIS A 253 PHE 0.024 0.001 PHE A 250 TYR 0.014 0.001 TYR E 351 ARG 0.002 0.000 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 233 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7695 (tp30) cc_final: 0.7242 (tp30) REVERT: B 168 TRP cc_start: 0.8113 (t-100) cc_final: 0.7573 (t-100) REVERT: B 245 GLU cc_start: 0.7892 (tp30) cc_final: 0.7539 (tp30) REVERT: B 404 GLN cc_start: 0.8171 (pp30) cc_final: 0.7835 (pp30) REVERT: C 20 LEU cc_start: 0.8644 (mt) cc_final: 0.8228 (mp) REVERT: C 37 MET cc_start: 0.8253 (mtt) cc_final: 0.7111 (tmm) REVERT: C 158 SER cc_start: 0.8155 (t) cc_final: 0.7927 (p) REVERT: C 308 TYR cc_start: 0.9086 (m-80) cc_final: 0.8457 (m-80) REVERT: C 375 MET cc_start: 0.6750 (mtm) cc_final: 0.6539 (mtm) REVERT: D 249 LYS cc_start: 0.8663 (ptmt) cc_final: 0.8390 (ptmm) REVERT: D 275 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7957 (t80) REVERT: D 382 TYR cc_start: 0.8599 (t80) cc_final: 0.8343 (t80) REVERT: E 381 GLN cc_start: 0.8048 (mm110) cc_final: 0.7770 (mm-40) REVERT: F 49 GLN cc_start: 0.6420 (tp40) cc_final: 0.6181 (tp40) REVERT: F 143 ASN cc_start: 0.5165 (OUTLIER) cc_final: 0.4538 (p0) REVERT: F 264 ARG cc_start: 0.7971 (mtp85) cc_final: 0.7705 (mtt90) REVERT: F 279 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7986 (p90) REVERT: F 323 TYR cc_start: 0.8465 (t80) cc_final: 0.8159 (t80) REVERT: F 354 VAL cc_start: 0.5602 (OUTLIER) cc_final: 0.5387 (p) REVERT: F 387 ARG cc_start: 0.5326 (ttp80) cc_final: 0.4561 (ttm110) REVERT: F 391 PHE cc_start: 0.5427 (m-80) cc_final: 0.4758 (m-80) outliers start: 55 outliers final: 41 residues processed: 274 average time/residue: 0.2595 time to fit residues: 108.6731 Evaluate side-chains 274 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 229 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN D 287 HIS E 287 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16429 Z= 0.215 Angle : 0.473 7.468 22166 Z= 0.256 Chirality : 0.039 0.219 2399 Planarity : 0.003 0.035 2678 Dihedral : 6.325 137.396 2256 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.03 % Allowed : 19.63 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.20), residues: 1845 helix: 1.92 (0.14), residues: 1300 sheet: 0.05 (0.52), residues: 100 loop : -0.38 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP F 23 HIS 0.018 0.001 HIS A 253 PHE 0.032 0.001 PHE E 250 TYR 0.017 0.001 TYR C 382 ARG 0.002 0.000 ARG E 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 231 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7701 (tp30) cc_final: 0.7247 (tp30) REVERT: B 168 TRP cc_start: 0.8122 (t-100) cc_final: 0.7584 (t-100) REVERT: B 245 GLU cc_start: 0.7876 (tp30) cc_final: 0.7512 (tp30) REVERT: B 298 ASP cc_start: 0.7630 (t0) cc_final: 0.7348 (p0) REVERT: B 404 GLN cc_start: 0.8182 (pp30) cc_final: 0.7844 (pp30) REVERT: C 18 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7651 (mtt90) REVERT: C 37 MET cc_start: 0.8300 (mtt) cc_final: 0.7130 (tmm) REVERT: C 158 SER cc_start: 0.8230 (t) cc_final: 0.7997 (p) REVERT: C 324 PHE cc_start: 0.8014 (t80) cc_final: 0.7791 (t80) REVERT: C 375 MET cc_start: 0.6758 (mtm) cc_final: 0.6530 (mtm) REVERT: C 393 PHE cc_start: 0.7432 (m-80) cc_final: 0.6971 (m-10) REVERT: D 249 LYS cc_start: 0.8657 (ptmt) cc_final: 0.8422 (ptmm) REVERT: D 382 TYR cc_start: 0.8605 (t80) cc_final: 0.8348 (t80) REVERT: E 381 GLN cc_start: 0.8046 (mm110) cc_final: 0.7791 (mm-40) REVERT: F 143 ASN cc_start: 0.5171 (OUTLIER) cc_final: 0.4584 (p0) REVERT: F 264 ARG cc_start: 0.7982 (mtp85) cc_final: 0.7688 (mtt90) REVERT: F 279 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.8007 (p90) REVERT: F 323 TYR cc_start: 0.8466 (t80) cc_final: 0.8153 (t80) REVERT: F 354 VAL cc_start: 0.5618 (OUTLIER) cc_final: 0.5404 (p) REVERT: F 387 ARG cc_start: 0.5389 (ttp80) cc_final: 0.4576 (ttm110) REVERT: F 391 PHE cc_start: 0.5375 (m-80) cc_final: 0.4702 (m-80) outliers start: 53 outliers final: 43 residues processed: 268 average time/residue: 0.2674 time to fit residues: 108.7433 Evaluate side-chains 271 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 225 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN D 119 HIS D 287 HIS E 287 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.183014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.133888 restraints weight = 21149.540| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.37 r_work: 0.3678 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16429 Z= 0.195 Angle : 0.476 9.946 22166 Z= 0.257 Chirality : 0.038 0.199 2399 Planarity : 0.003 0.035 2678 Dihedral : 6.178 134.448 2256 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.98 % Allowed : 19.52 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.20), residues: 1845 helix: 1.93 (0.14), residues: 1300 sheet: 0.11 (0.50), residues: 106 loop : -0.37 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP F 23 HIS 0.016 0.001 HIS A 253 PHE 0.041 0.001 PHE E 250 TYR 0.014 0.001 TYR E 351 ARG 0.002 0.000 ARG E 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3734.04 seconds wall clock time: 69 minutes 51.58 seconds (4191.58 seconds total)