Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 22:20:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f74_28894/04_2023/8f74_28894_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f74_28894/04_2023/8f74_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_28894/04_2023/8f74_28894.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f74_28894/04_2023/8f74_28894.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f74_28894/04_2023/8f74_28894_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f74_28894/04_2023/8f74_28894_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 75 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: 80 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: 21 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: 55 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: 85 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: 72 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: 8.81, per 1000 atoms: 0.55 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 2.3 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: 1.27 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: 4.84 Time building geometry restraints manager: 7.02 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: 9389 34.77 - 69.54: 299 69.54 - 104.31: 17 104.31 - 139.08: 1 139.08 - 173.86: 4 Dihedral angle restraints: 9710 sinusoidal: 4058 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=" N PEE A 901 " pdb=" C4 PEE A 901 " pdb=" C5 PEE A 901 " pdb=" O4P PEE A 901 " ideal model delta sinusoidal sigma weight residual -56.97 99.02 -155.99 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 9707 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: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 16.340 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 41.550 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.070 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.110 ------------------------------------------------------------------------------- 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 : 16.783 173.856 5999 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 % 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 *********************** 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 : 1.882 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.2769 time to fit residues: 107.0744 Evaluate side-chains 216 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.936 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6815 ------------------------------------------------------------------------------- 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: 1.9990 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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: 0.7872 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.072 16429 Z= 0.435 Angle : 0.580 10.312 22166 Z= 0.314 Chirality : 0.042 0.160 2399 Planarity : 0.004 0.038 2678 Dihedral : 9.271 165.524 2228 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 3.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 1845 helix: 1.44 (0.14), residues: 1300 sheet: -0.39 (0.51), residues: 106 loop : -0.91 (0.30), residues: 439 *********************** 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 298 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 229 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 41 residues processed: 275 average time/residue: 0.2600 time to fit residues: 109.3054 Evaluate side-chains 254 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 213 time to evaluate : 2.098 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.1944 time to fit residues: 16.8928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 113 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 165 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7829 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 16429 Z= 0.246 Angle : 0.471 6.286 22166 Z= 0.258 Chirality : 0.038 0.199 2399 Planarity : 0.003 0.034 2678 Dihedral : 7.937 161.415 2228 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 2.06 % 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: 1.32 (0.19), residues: 1845 helix: 1.55 (0.14), residues: 1305 sheet: -0.23 (0.52), residues: 107 loop : -0.80 (0.30), residues: 433 *********************** 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 267 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 231 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 14 residues processed: 251 average time/residue: 0.2729 time to fit residues: 103.8290 Evaluate side-chains 224 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 210 time to evaluate : 1.838 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2142 time to fit residues: 7.3786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 86 optimal weight: 0.0770 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 167 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS B 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1683 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= 0.166 Angle : 0.437 5.061 22166 Z= 0.239 Chirality : 0.037 0.188 2399 Planarity : 0.003 0.030 2678 Dihedral : 7.317 157.005 2228 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.19), residues: 1845 helix: 1.75 (0.14), residues: 1301 sheet: 0.02 (0.52), residues: 107 loop : -0.69 (0.30), residues: 437 *********************** 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 269 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 238 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 16 residues processed: 257 average time/residue: 0.2742 time to fit residues: 105.8111 Evaluate side-chains 238 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 222 time to evaluate : 1.800 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1848 time to fit residues: 7.4828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 2 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16429 Z= 0.217 Angle : 0.458 6.798 22166 Z= 0.250 Chirality : 0.038 0.190 2399 Planarity : 0.003 0.030 2678 Dihedral : 7.169 157.818 2228 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 2.00 % 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: 1.68 (0.19), residues: 1845 helix: 1.79 (0.14), residues: 1297 sheet: 0.03 (0.51), residues: 107 loop : -0.57 (0.30), residues: 441 *********************** 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 265 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 230 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 9 residues processed: 249 average time/residue: 0.2750 time to fit residues: 103.4848 Evaluate side-chains 223 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 214 time to evaluate : 1.990 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1487 time to fit residues: 5.2455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 178 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 E 287 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2000 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= 0.212 Angle : 0.461 7.365 22166 Z= 0.251 Chirality : 0.038 0.198 2399 Planarity : 0.003 0.029 2678 Dihedral : 6.976 157.197 2228 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 1.66 % 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: 1.74 (0.20), residues: 1845 helix: 1.82 (0.14), residues: 1296 sheet: 0.16 (0.51), residues: 107 loop : -0.54 (0.31), residues: 442 *********************** 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 258 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 229 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 243 average time/residue: 0.2892 time to fit residues: 105.4656 Evaluate side-chains 227 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 210 time to evaluate : 1.788 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2259 time to fit residues: 8.6334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 287 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2126 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= 0.207 Angle : 0.464 7.896 22166 Z= 0.252 Chirality : 0.038 0.211 2399 Planarity : 0.003 0.029 2678 Dihedral : 6.734 155.856 2228 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 1.32 % 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: 1.80 (0.20), residues: 1845 helix: 1.87 (0.14), residues: 1298 sheet: 0.15 (0.51), residues: 107 loop : -0.51 (0.31), residues: 440 *********************** 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 251 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 228 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 6 residues processed: 243 average time/residue: 0.2756 time to fit residues: 101.2339 Evaluate side-chains 221 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 215 time to evaluate : 1.910 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1463 time to fit residues: 4.2992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 105 optimal weight: 9.9990 chunk 53 optimal weight: 0.0670 chunk 34 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2161 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= 0.173 Angle : 0.461 8.639 22166 Z= 0.250 Chirality : 0.038 0.171 2399 Planarity : 0.003 0.029 2678 Dihedral : 6.387 152.311 2228 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.86 % 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: 1.88 (0.20), residues: 1845 helix: 1.91 (0.14), residues: 1299 sheet: 0.22 (0.51), residues: 107 loop : -0.44 (0.31), residues: 439 *********************** 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 244 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 229 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 239 average time/residue: 0.2611 time to fit residues: 94.8223 Evaluate side-chains 227 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 222 time to evaluate : 1.672 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2137 time to fit residues: 4.0370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN B 66 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN D 119 HIS D 287 HIS E 155 HIS E 287 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 16429 Z= 0.274 Angle : 0.508 8.250 22166 Z= 0.275 Chirality : 0.040 0.216 2399 Planarity : 0.003 0.033 2678 Dihedral : 6.586 157.287 2228 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.57 % 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: 1.72 (0.20), residues: 1845 helix: 1.81 (0.14), residues: 1298 sheet: 0.15 (0.51), residues: 106 loop : -0.55 (0.31), residues: 441 *********************** 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 234 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 224 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 230 average time/residue: 0.2830 time to fit residues: 98.3201 Evaluate side-chains 220 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 216 time to evaluate : 1.805 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1499 time to fit residues: 3.6307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 145 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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: 0.7806 moved from start: 0.2340 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= 0.210 Angle : 0.486 9.933 22166 Z= 0.264 Chirality : 0.038 0.169 2399 Planarity : 0.003 0.032 2678 Dihedral : 6.297 153.711 2228 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 0.34 % 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: 1.79 (0.20), residues: 1845 helix: 1.87 (0.14), residues: 1296 sheet: 0.21 (0.51), residues: 106 loop : -0.55 (0.30), residues: 443 ********************** 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 225 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 219 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 223 average time/residue: 0.2806 time to fit residues: 94.7667 Evaluate side-chains 217 residues out of total 1747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 214 time to evaluate : 1.843 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3318 time to fit residues: 3.9596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 134 optimal weight: 0.9980 chunk 21 optimal weight: 0.0000 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.0060 chunk 128 optimal weight: 1.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.172713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131346 restraints weight = 20615.069| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.05 r_work: 0.3408 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16429 Z= 0.169 Angle : 0.480 9.651 22166 Z= 0.260 Chirality : 0.038 0.216 2399 Planarity : 0.003 0.032 2678 Dihedral : 5.926 147.679 2228 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.29 % 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: 1.89 (0.20), residues: 1845 helix: 1.91 (0.14), residues: 1298 sheet: 0.22 (0.51), residues: 107 loop : -0.43 (0.31), residues: 440 =============================================================================== Job complete usr+sys time: 3455.42 seconds wall clock time: 63 minutes 44.72 seconds (3824.72 seconds total)