Starting phenix.real_space_refine on Fri Feb 16 19:17:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr8_27674/02_2024/8dr8_27674_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr8_27674/02_2024/8dr8_27674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr8_27674/02_2024/8dr8_27674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr8_27674/02_2024/8dr8_27674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr8_27674/02_2024/8dr8_27674_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr8_27674/02_2024/8dr8_27674_updated.pdb" } resolution = 3.04 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= 0.001 sd= 0.078 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 9 5.49 5 S 106 5.16 5 C 10800 2.51 5 N 2525 2.21 5 O 2830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 102": "OD1" <-> "OD2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 102": "OD1" <-> "OD2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 358": "OE1" <-> "OE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 245": "OE1" <-> "OE2" Residue "E PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 256": "OE1" <-> "OE2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 298": "OD1" <-> "OD2" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 380": "OD1" <-> "OD2" Residue "E TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 177": "OE1" <-> "OE2" Residue "F GLU 243": "OE1" <-> "OE2" Residue "F ASP 299": "OD1" <-> "OD2" Residue "F PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F ASP 361": "OD1" <-> "OD2" Residue "F ASP 365": "OD1" <-> "OD2" Residue "F TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16270 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2671 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain breaks: 2 Chain: "B" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2667 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Chain: "C" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2519 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Chain: "D" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2653 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 2651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2651 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 46 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: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 87 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 88 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: 8.47, per 1000 atoms: 0.52 Number of scatterers: 16270 At special positions: 0 Unit cell: (95.368, 107.944, 138.336, 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 9 15.00 O 2830 8.00 N 2525 7.00 C 10800 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=2.04 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: 6.59 Conformation dependent library (CDL) restraints added in 2.8 seconds 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 6 sheets defined 68.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 17 through 20 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: 4.203A 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 288 removed outlier: 4.729A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASN A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 345 removed outlier: 4.278A pdb=" N THR A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.941A 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 393 removed outlier: 4.052A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'B' and resid 17 through 20 Processing helix chain 'B' and resid 23 through 48 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: 4.559A 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 164 removed outlier: 3.917A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 removed outlier: 3.647A 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 260 through 288 removed outlier: 4.778A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ASN B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 342 removed outlier: 4.095A pdb=" N PHE B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) 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: 4.267A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.977A 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 23 through 48 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: 4.420A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.719A 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 241 through 254 Processing helix chain 'C' and resid 259 through 288 removed outlier: 3.577A pdb=" N PHE C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASN C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 343 removed outlier: 3.500A pdb=" N ALA C 322 " --> pdb=" O PHE C 318 " (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 391 Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'D' and resid 16 through 20 removed outlier: 3.959A 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 145 Proline residue: D 126 - end of helix removed outlier: 4.706A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 234 through 256 removed outlier: 3.644A pdb=" N GLU D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 288 removed outlier: 4.923A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASN D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 345 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 370 through 382 Processing helix chain 'D' and resid 384 through 393 removed outlier: 4.682A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 409 Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' 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: 4.499A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 164 Processing helix chain 'E' and resid 167 through 174 removed outlier: 3.858A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 254 Processing helix chain 'E' and resid 260 through 288 removed outlier: 4.720A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASN E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 344 removed outlier: 3.542A pdb=" N ALA E 322 " --> pdb=" O PHE E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 357 removed outlier: 4.239A pdb=" N ARG E 357 " --> pdb=" O GLU E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 382 Processing helix chain 'E' and resid 384 through 393 removed outlier: 4.164A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.784A 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 46 Processing helix chain 'F' and resid 105 through 118 Processing helix chain 'F' and resid 122 through 142 Proline residue: F 128 - end of helix Processing helix chain 'F' and resid 149 through 166 Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 233 through 252 Processing helix chain 'F' and resid 257 through 286 removed outlier: 4.843A pdb=" N SER F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 343 Processing helix chain 'F' and resid 352 through 357 removed outlier: 4.191A pdb=" N GLU F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 380 Processing helix chain 'F' and resid 382 through 391 removed outlier: 4.651A pdb=" N VAL F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 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 Processing sheet with id= C, first strand: chain 'C' and resid 53 through 56 Processing sheet with id= D, first strand: chain 'D' and resid 52 through 56 Processing sheet with id= E, first strand: chain 'E' and resid 53 through 56 Processing sheet with id= F, first strand: chain 'F' and resid 52 through 56 968 hydrogen bonds defined for protein. 2799 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: 4.67 Time building geometry restraints manager: 7.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2697 1.33 - 1.45: 4647 1.45 - 1.57: 9172 1.57 - 1.70: 10 1.70 - 1.82: 160 Bond restraints: 16686 Sorted by residual: bond pdb=" C10 PEE F 902 " pdb=" O4 PEE F 902 " ideal model delta sigma weight residual 1.206 1.358 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C10 PEE E 902 " pdb=" O4 PEE E 902 " ideal model delta sigma weight residual 1.206 1.358 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C10 PEE F 903 " pdb=" O4 PEE F 903 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C10 PEE C 902 " pdb=" O4 PEE C 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" C10 PEE D 902 " pdb=" O4 PEE D 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 16681 not shown) Histogram of bond angle deviations from ideal: 90.62 - 99.34: 9 99.34 - 108.06: 624 108.06 - 116.78: 10443 116.78 - 125.50: 11065 125.50 - 134.23: 307 Bond angle restraints: 22448 Sorted by residual: angle pdb=" C ASN F 368 " pdb=" CA ASN F 368 " pdb=" CB ASN F 368 " ideal model delta sigma weight residual 116.63 109.95 6.68 1.16e+00 7.43e-01 3.32e+01 angle pdb=" C ASN E 370 " pdb=" CA ASN E 370 " pdb=" CB ASN E 370 " ideal model delta sigma weight residual 116.63 110.17 6.46 1.16e+00 7.43e-01 3.10e+01 angle pdb=" CA ASN F 368 " pdb=" C ASN F 368 " pdb=" N ASP F 369 " ideal model delta sigma weight residual 119.63 115.78 3.85 8.10e-01 1.52e+00 2.26e+01 angle pdb=" O1P PEE D 901 " pdb=" P PEE D 901 " pdb=" O2P PEE D 901 " ideal model delta sigma weight residual 119.43 133.34 -13.91 3.00e+00 1.11e-01 2.15e+01 angle pdb=" O1P PEE D 904 " pdb=" P PEE D 904 " pdb=" O2P PEE D 904 " ideal model delta sigma weight residual 119.43 133.29 -13.86 3.00e+00 1.11e-01 2.14e+01 ... (remaining 22443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 9534 35.76 - 71.51: 384 71.51 - 107.27: 30 107.27 - 143.02: 19 143.02 - 178.78: 16 Dihedral angle restraints: 9983 sinusoidal: 4338 harmonic: 5645 Sorted by residual: dihedral pdb=" CB CYS C 57 " pdb=" SG CYS C 57 " pdb=" SG CYS C 65 " pdb=" CB CYS C 65 " ideal model delta sinusoidal sigma weight residual -86.00 -6.58 -79.42 1 1.00e+01 1.00e-02 7.84e+01 dihedral pdb=" CB CYS E 113 " pdb=" SG CYS E 113 " pdb=" SG CYS E 295 " pdb=" CB CYS E 295 " ideal model delta sinusoidal sigma weight residual 93.00 48.87 44.13 1 1.00e+01 1.00e-02 2.71e+01 dihedral pdb=" CB CYS D 113 " pdb=" SG CYS D 113 " pdb=" SG CYS D 295 " pdb=" CB CYS D 295 " ideal model delta sinusoidal sigma weight residual 93.00 51.95 41.05 1 1.00e+01 1.00e-02 2.36e+01 ... (remaining 9980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2280 0.084 - 0.168: 119 0.168 - 0.252: 3 0.252 - 0.336: 1 0.336 - 0.420: 7 Chirality restraints: 2410 Sorted by residual: chirality pdb=" C2 PEE D 901 " pdb=" C1 PEE D 901 " pdb=" C3 PEE D 901 " pdb=" O2 PEE D 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C2 PEE D 904 " pdb=" C1 PEE D 904 " pdb=" C3 PEE D 904 " pdb=" O2 PEE D 904 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C2 PEE C 901 " pdb=" C1 PEE C 901 " pdb=" C3 PEE C 901 " pdb=" O2 PEE C 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 2407 not shown) Planarity restraints: 2682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 23 " -0.023 2.00e-02 2.50e+03 2.21e-02 1.23e+01 pdb=" CG TRP C 23 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP C 23 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 23 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 23 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 23 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 23 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 390 " -0.012 2.00e-02 2.50e+03 1.92e-02 6.48e+00 pdb=" CG PHE E 390 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE E 390 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE E 390 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE E 390 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 390 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 390 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 170 " -0.011 2.00e-02 2.50e+03 1.60e-02 6.42e+00 pdb=" CG TRP F 170 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP F 170 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP F 170 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 170 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 170 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 170 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 170 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 170 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 170 " 0.001 2.00e-02 2.50e+03 ... (remaining 2679 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2018 2.75 - 3.29: 15778 3.29 - 3.83: 28676 3.83 - 4.36: 32375 4.36 - 4.90: 57113 Nonbonded interactions: 135960 Sorted by model distance: nonbonded pdb=" O SER F 168 " pdb=" OG1 THR F 171 " model vdw 2.216 2.440 nonbonded pdb=" O ILE B 356 " pdb=" OG SER B 360 " model vdw 2.240 2.440 nonbonded pdb=" O THR A 44 " pdb=" OG1 THR A 48 " model vdw 2.260 2.440 nonbonded pdb=" NE2 GLN B 49 " pdb=" O VAL C 47 " model vdw 2.276 2.520 nonbonded pdb=" OE1 GLN C 46 " pdb=" OH TYR C 127 " model vdw 2.276 2.440 ... (remaining 135955 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 240 through \ 402 or (resid 902 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 )) 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 C1 \ 7 or name O2 or name O4 )))) selection = (chain 'B' and (resid 15 through 68 or resid 93 through 175 or resid 240 through \ 402 or (resid 902 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 )) or resid 903)) 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 ) \ ) or (resid 902 and (name C10 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C16 or name C17 or name O2 or name O4 )))) selection = (chain 'D' and (resid 15 through 175 or resid 240 through 402 or resid 902 or (r \ esid 903 and (name C10 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name O2 or name O4 )))) selection = (chain 'E' and (resid 15 through 175 or resid 240 through 402 or (resid 902 and \ (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name O2 or name O4 )) 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: 3.960 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: 15.900 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 44.510 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.080 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 0.007 0.152 16686 Z= 0.420 Angle : 0.817 13.914 22448 Z= 0.398 Chirality : 0.047 0.420 2410 Planarity : 0.005 0.062 2682 Dihedral : 20.916 178.780 6276 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.17 % Allowed : 21.55 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 1842 helix: 1.13 (0.13), residues: 1290 sheet: 0.88 (0.54), residues: 104 loop : -0.86 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP C 23 HIS 0.020 0.002 HIS A 253 PHE 0.043 0.002 PHE E 390 TYR 0.036 0.001 TYR C 284 ARG 0.013 0.001 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 245 time to evaluate : 1.847 Fit side-chains revert: symmetry clash REVERT: D 27 PHE cc_start: 0.7135 (m-10) cc_final: 0.6783 (m-10) REVERT: D 375 MET cc_start: 0.8240 (mtm) cc_final: 0.7989 (mtm) REVERT: E 241 LYS cc_start: 0.7520 (mmmt) cc_final: 0.6617 (tppt) REVERT: E 245 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6782 (mm-30) REVERT: F 243 GLU cc_start: 0.7778 (mp0) cc_final: 0.7480 (mp0) outliers start: 3 outliers final: 2 residues processed: 245 average time/residue: 0.2588 time to fit residues: 98.4693 Evaluate side-chains 228 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 226 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain E residue 52 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 144 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 87 optimal weight: 0.0770 chunk 107 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN D 66 ASN D 253 HIS F 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16686 Z= 0.181 Angle : 0.448 7.782 22448 Z= 0.240 Chirality : 0.037 0.145 2410 Planarity : 0.003 0.038 2682 Dihedral : 15.763 170.662 2523 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.95 % Allowed : 20.92 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.19), residues: 1842 helix: 1.91 (0.14), residues: 1297 sheet: 0.88 (0.54), residues: 93 loop : -0.69 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 23 HIS 0.008 0.001 HIS D 253 PHE 0.011 0.001 PHE B 250 TYR 0.014 0.001 TYR D 382 ARG 0.007 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 244 time to evaluate : 1.898 Fit side-chains revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7342 (mtm180) cc_final: 0.6760 (mtp-110) REVERT: A 396 GLU cc_start: 0.7379 (pm20) cc_final: 0.7173 (pm20) REVERT: A 400 ASN cc_start: 0.6698 (m-40) cc_final: 0.6495 (m110) REVERT: C 375 MET cc_start: 0.6334 (mtm) cc_final: 0.5878 (mtm) REVERT: D 27 PHE cc_start: 0.7030 (m-10) cc_final: 0.6709 (m-10) REVERT: E 245 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6770 (mm-30) REVERT: F 243 GLU cc_start: 0.7828 (mp0) cc_final: 0.7602 (mp0) REVERT: F 247 LYS cc_start: 0.8598 (tttt) cc_final: 0.7902 (tptt) outliers start: 34 outliers final: 21 residues processed: 264 average time/residue: 0.2557 time to fit residues: 104.2016 Evaluate side-chains 245 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 224 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 149 optimal weight: 0.0470 chunk 165 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 HIS ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN F 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16686 Z= 0.350 Angle : 0.518 7.400 22448 Z= 0.281 Chirality : 0.040 0.132 2410 Planarity : 0.003 0.031 2682 Dihedral : 14.657 167.073 2518 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.27 % Allowed : 20.80 % Favored : 75.93 % 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: 1.59 (0.19), residues: 1842 helix: 1.75 (0.14), residues: 1300 sheet: 0.54 (0.52), residues: 106 loop : -0.90 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 23 HIS 0.007 0.001 HIS D 253 PHE 0.017 0.002 PHE E 390 TYR 0.013 0.002 TYR A 351 ARG 0.007 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 228 time to evaluate : 2.074 Fit side-chains REVERT: A 262 ARG cc_start: 0.7419 (mtm180) cc_final: 0.6767 (mtp-110) REVERT: A 275 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7770 (t80) REVERT: A 400 ASN cc_start: 0.6721 (m-40) cc_final: 0.6519 (m110) REVERT: B 102 ASP cc_start: 0.8369 (m-30) cc_final: 0.8093 (m-30) REVERT: C 46 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7794 (tm-30) REVERT: C 308 TYR cc_start: 0.8809 (m-80) cc_final: 0.8431 (m-80) REVERT: C 351 TYR cc_start: 0.6055 (t80) cc_final: 0.5822 (t80) REVERT: C 375 MET cc_start: 0.6480 (mtm) cc_final: 0.6151 (mtm) REVERT: C 385 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6985 (tp) REVERT: D 372 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.6492 (t80) REVERT: D 375 MET cc_start: 0.8296 (mtm) cc_final: 0.7769 (mtm) REVERT: E 241 LYS cc_start: 0.7560 (mmmt) cc_final: 0.6324 (tppt) REVERT: E 245 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7026 (mm-30) REVERT: E 263 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7389 (mp) REVERT: F 355 ARG cc_start: 0.6062 (ttm-80) cc_final: 0.5616 (ttm-80) outliers start: 57 outliers final: 35 residues processed: 269 average time/residue: 0.2530 time to fit residues: 105.3835 Evaluate side-chains 253 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 214 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 167 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 87 optimal weight: 0.0470 chunk 159 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS F 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16686 Z= 0.157 Angle : 0.429 7.680 22448 Z= 0.232 Chirality : 0.037 0.180 2410 Planarity : 0.003 0.028 2682 Dihedral : 12.852 151.222 2518 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.69 % Allowed : 21.49 % Favored : 75.82 % 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 (0.19), residues: 1842 helix: 2.03 (0.14), residues: 1293 sheet: 0.89 (0.53), residues: 99 loop : -0.81 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 170 HIS 0.009 0.001 HIS D 253 PHE 0.017 0.001 PHE E 390 TYR 0.013 0.001 TYR D 338 ARG 0.003 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 236 time to evaluate : 1.988 Fit side-chains revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7327 (mtm180) cc_final: 0.6767 (mtp-110) REVERT: A 275 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7716 (t80) REVERT: A 357 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7069 (ttp80) REVERT: A 396 GLU cc_start: 0.7552 (pm20) cc_final: 0.7267 (pm20) REVERT: C 248 LYS cc_start: 0.5295 (mmtt) cc_final: 0.4482 (ptpt) REVERT: C 375 MET cc_start: 0.6438 (mtm) cc_final: 0.6204 (mtm) REVERT: D 134 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8341 (mm) REVERT: D 372 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.6301 (t80) REVERT: D 375 MET cc_start: 0.8251 (mtm) cc_final: 0.7730 (mtm) REVERT: E 241 LYS cc_start: 0.7522 (mmmt) cc_final: 0.7168 (mmmt) REVERT: E 244 PHE cc_start: 0.6155 (m-80) cc_final: 0.5937 (m-80) REVERT: E 245 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6892 (mm-30) REVERT: E 263 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7302 (mp) REVERT: F 355 ARG cc_start: 0.5879 (ttm-80) cc_final: 0.5654 (ttm-80) outliers start: 47 outliers final: 29 residues processed: 269 average time/residue: 0.2593 time to fit residues: 109.0339 Evaluate side-chains 255 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 221 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 151 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16686 Z= 0.175 Angle : 0.431 8.139 22448 Z= 0.232 Chirality : 0.037 0.150 2410 Planarity : 0.003 0.027 2682 Dihedral : 11.934 151.493 2518 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.75 % Allowed : 22.01 % Favored : 75.24 % 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 (0.19), residues: 1842 helix: 2.08 (0.14), residues: 1296 sheet: 0.82 (0.52), residues: 100 loop : -0.80 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 170 HIS 0.012 0.001 HIS D 253 PHE 0.018 0.001 PHE E 390 TYR 0.018 0.001 TYR C 382 ARG 0.003 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 241 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7336 (mtm180) cc_final: 0.6762 (mtp-110) REVERT: A 275 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7718 (t80) REVERT: A 357 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7074 (ttp80) REVERT: B 51 LYS cc_start: 0.8409 (ptmt) cc_final: 0.8194 (ptmt) REVERT: B 104 HIS cc_start: 0.8979 (OUTLIER) cc_final: 0.8266 (t70) REVERT: C 248 LYS cc_start: 0.5137 (mmtt) cc_final: 0.4252 (ptpt) REVERT: C 375 MET cc_start: 0.6463 (mtm) cc_final: 0.6255 (mtm) REVERT: D 134 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8323 (mm) REVERT: D 372 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6364 (t80) REVERT: D 375 MET cc_start: 0.8279 (mtm) cc_final: 0.7745 (mtm) REVERT: E 263 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7274 (mp) REVERT: F 18 ARG cc_start: 0.6719 (mpp-170) cc_final: 0.6505 (mpp-170) outliers start: 48 outliers final: 36 residues processed: 276 average time/residue: 0.2609 time to fit residues: 111.4241 Evaluate side-chains 265 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 223 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL 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: 1.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 0.0070 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN D 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.004 0.039 16686 Z= 0.264 Angle : 0.471 7.374 22448 Z= 0.254 Chirality : 0.039 0.180 2410 Planarity : 0.003 0.026 2682 Dihedral : 11.561 148.125 2518 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.61 % Allowed : 21.43 % Favored : 74.96 % 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: 1.86 (0.19), residues: 1842 helix: 1.95 (0.14), residues: 1300 sheet: 0.59 (0.51), residues: 106 loop : -0.79 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 170 HIS 0.010 0.001 HIS D 253 PHE 0.020 0.001 PHE E 390 TYR 0.015 0.001 TYR C 325 ARG 0.004 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 220 time to evaluate : 1.962 Fit side-chains revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7812 (t80) REVERT: B 102 ASP cc_start: 0.8292 (m-30) cc_final: 0.8004 (m-30) REVERT: C 18 ARG cc_start: 0.6867 (ptp-110) cc_final: 0.6640 (ptm160) REVERT: D 372 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.6435 (t80) REVERT: E 245 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6695 (mm-30) REVERT: E 263 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7399 (mp) REVERT: F 18 ARG cc_start: 0.7040 (mpp-170) cc_final: 0.6745 (mpp-170) REVERT: F 370 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.7088 (t80) outliers start: 63 outliers final: 49 residues processed: 267 average time/residue: 0.2782 time to fit residues: 114.3684 Evaluate side-chains 260 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 207 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 108 optimal weight: 0.3980 chunk 81 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN D 253 HIS E 312 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16686 Z= 0.168 Angle : 0.438 8.627 22448 Z= 0.235 Chirality : 0.037 0.156 2410 Planarity : 0.003 0.026 2682 Dihedral : 10.754 142.220 2518 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.44 % Allowed : 21.78 % Favored : 74.79 % 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 (0.19), residues: 1842 helix: 2.07 (0.14), residues: 1293 sheet: 0.80 (0.52), residues: 99 loop : -0.72 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 170 HIS 0.009 0.001 HIS D 253 PHE 0.022 0.001 PHE E 390 TYR 0.012 0.001 TYR D 338 ARG 0.004 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 237 time to evaluate : 2.019 Fit side-chains revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7324 (mtm180) cc_final: 0.6817 (mtp-110) REVERT: A 275 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7799 (t80) REVERT: B 51 LYS cc_start: 0.8432 (ptmt) cc_final: 0.8206 (ptmt) REVERT: B 102 ASP cc_start: 0.8199 (m-30) cc_final: 0.7898 (m-30) REVERT: B 104 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.8219 (t70) REVERT: C 102 ASP cc_start: 0.8113 (m-30) cc_final: 0.7885 (m-30) REVERT: D 134 LEU cc_start: 0.8465 (mt) cc_final: 0.8253 (mm) REVERT: D 375 MET cc_start: 0.8207 (mtm) cc_final: 0.7740 (mtm) REVERT: E 241 LYS cc_start: 0.7562 (mmmt) cc_final: 0.6657 (tppt) REVERT: E 244 PHE cc_start: 0.5985 (m-80) cc_final: 0.5729 (m-80) REVERT: E 245 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6619 (mm-30) REVERT: E 263 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7277 (mp) REVERT: F 18 ARG cc_start: 0.7018 (mpp-170) cc_final: 0.6749 (mpp-170) outliers start: 60 outliers final: 47 residues processed: 279 average time/residue: 0.2607 time to fit residues: 112.2799 Evaluate side-chains 275 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 225 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 105 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 400 ASN D 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16686 Z= 0.270 Angle : 0.485 9.245 22448 Z= 0.262 Chirality : 0.039 0.184 2410 Planarity : 0.003 0.026 2682 Dihedral : 10.392 134.838 2518 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.72 % Allowed : 21.60 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.19), residues: 1842 helix: 1.92 (0.14), residues: 1302 sheet: 0.46 (0.52), residues: 101 loop : -0.72 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 170 HIS 0.011 0.001 HIS D 253 PHE 0.023 0.001 PHE E 390 TYR 0.013 0.001 TYR D 281 ARG 0.004 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 224 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7385 (mtm180) cc_final: 0.6864 (mtp-110) REVERT: A 275 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7805 (t80) REVERT: B 102 ASP cc_start: 0.8298 (m-30) cc_final: 0.8003 (m-30) REVERT: B 104 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.8330 (t70) REVERT: C 284 TYR cc_start: 0.7403 (t80) cc_final: 0.7092 (t80) REVERT: D 372 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.6498 (t80) REVERT: E 241 LYS cc_start: 0.7625 (mmmt) cc_final: 0.7344 (mmmt) REVERT: E 245 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6666 (mm-30) REVERT: E 263 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7394 (mp) outliers start: 65 outliers final: 51 residues processed: 270 average time/residue: 0.2648 time to fit residues: 109.8132 Evaluate side-chains 272 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 217 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 165 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 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 400 ASN D 253 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16686 Z= 0.200 Angle : 0.465 10.258 22448 Z= 0.251 Chirality : 0.038 0.330 2410 Planarity : 0.003 0.026 2682 Dihedral : 9.813 125.346 2518 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.21 % Allowed : 22.29 % Favored : 74.50 % 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: 1.95 (0.19), residues: 1842 helix: 2.00 (0.14), residues: 1293 sheet: 0.55 (0.52), residues: 100 loop : -0.61 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP F 170 HIS 0.008 0.001 HIS D 253 PHE 0.025 0.001 PHE E 390 TYR 0.015 0.001 TYR E 308 ARG 0.004 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 234 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7329 (mtm180) cc_final: 0.6808 (mtp-110) REVERT: A 275 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7800 (t80) REVERT: B 102 ASP cc_start: 0.8237 (m-30) cc_final: 0.7938 (m-30) REVERT: B 104 HIS cc_start: 0.8989 (OUTLIER) cc_final: 0.8323 (t70) REVERT: C 284 TYR cc_start: 0.7361 (t80) cc_final: 0.7071 (t80) REVERT: D 372 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6387 (t80) REVERT: D 375 MET cc_start: 0.8245 (mtm) cc_final: 0.7752 (mtm) REVERT: E 241 LYS cc_start: 0.7577 (mmmt) cc_final: 0.7322 (mmmt) REVERT: E 245 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6725 (mm-30) REVERT: E 263 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7369 (mp) outliers start: 56 outliers final: 47 residues processed: 274 average time/residue: 0.2617 time to fit residues: 109.9318 Evaluate side-chains 278 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 227 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 145 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 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 400 ASN D 253 HIS D 404 GLN D 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 0.048 16686 Z= 0.200 Angle : 0.471 11.148 22448 Z= 0.252 Chirality : 0.039 0.302 2410 Planarity : 0.003 0.028 2682 Dihedral : 9.633 119.887 2518 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.38 % Allowed : 22.41 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.19), residues: 1842 helix: 2.00 (0.14), residues: 1291 sheet: 0.57 (0.52), residues: 100 loop : -0.61 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 168 HIS 0.011 0.001 HIS D 253 PHE 0.026 0.001 PHE E 390 TYR 0.021 0.001 TYR C 382 ARG 0.005 0.000 ARG F 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 228 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.7334 (mtm180) cc_final: 0.6811 (mtp-110) REVERT: A 275 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7784 (t80) REVERT: A 404 GLN cc_start: 0.8177 (tp-100) cc_final: 0.7956 (tp-100) REVERT: B 102 ASP cc_start: 0.8225 (m-30) cc_final: 0.7923 (m-30) REVERT: B 104 HIS cc_start: 0.8989 (OUTLIER) cc_final: 0.8286 (t70) REVERT: B 350 LYS cc_start: 0.8337 (mtpt) cc_final: 0.7872 (pttt) REVERT: C 284 TYR cc_start: 0.7360 (t80) cc_final: 0.7084 (t80) REVERT: D 372 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6373 (t80) REVERT: D 375 MET cc_start: 0.8234 (mtm) cc_final: 0.7763 (mtm) REVERT: E 30 TYR cc_start: 0.8275 (m-80) cc_final: 0.7865 (m-80) REVERT: E 241 LYS cc_start: 0.7564 (mmmt) cc_final: 0.7304 (mmmt) REVERT: E 245 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6764 (mm-30) REVERT: E 263 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7358 (mp) outliers start: 59 outliers final: 51 residues processed: 271 average time/residue: 0.2559 time to fit residues: 107.2684 Evaluate side-chains 283 residues out of total 1745 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 228 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 372 PHE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 113 GLN Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 chunk 134 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 150 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 128 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN D 253 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.184445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.135619 restraints weight = 19681.982| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.35 r_work: 0.3623 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16686 Z= 0.156 Angle : 0.461 12.186 22448 Z= 0.245 Chirality : 0.038 0.297 2410 Planarity : 0.003 0.027 2682 Dihedral : 9.277 112.963 2518 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.87 % Allowed : 22.98 % Favored : 74.15 % 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: 2.07 (0.19), residues: 1842 helix: 2.11 (0.14), residues: 1287 sheet: 0.74 (0.53), residues: 99 loop : -0.61 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 168 HIS 0.010 0.001 HIS D 253 PHE 0.026 0.001 PHE D 244 TYR 0.037 0.001 TYR C 325 ARG 0.005 0.000 ARG F 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3855.19 seconds wall clock time: 70 minutes 44.01 seconds (4244.01 seconds total)