Starting phenix.real_space_refine on Sun Mar 17 02:32:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drk_27677/03_2024/8drk_27677_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drk_27677/03_2024/8drk_27677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drk_27677/03_2024/8drk_27677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drk_27677/03_2024/8drk_27677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drk_27677/03_2024/8drk_27677_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drk_27677/03_2024/8drk_27677_updated.pdb" } resolution = 2.95 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= 0.085 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 10903 2.51 5 N 2556 2.21 5 O 2869 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 ASP 67": "OD1" <-> "OD2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 165": "OD1" <-> "OD2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 165": "OD1" <-> "OD2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D ASP 102": "OD1" <-> "OD2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D ASP 380": "OD1" <-> "OD2" Residue "D TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 29": "OD1" <-> "OD2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 236": "OE1" <-> "OE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 245": "OE1" <-> "OE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 354": "OE1" <-> "OE2" Residue "E GLU 358": "OE1" <-> "OE2" Residue "E GLU 396": "OE1" <-> "OE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 234": "OE1" <-> "OE2" Residue "F TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 296": "OD1" <-> "OD2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 348": "OE1" <-> "OE2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F ASP 378": "OD1" <-> "OD2" Residue "F ASP 381": "OD1" <-> "OD2" Residue "F PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16443 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: 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: "C" 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: "D" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2646 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" 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: "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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 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: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 89 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 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: 8.56, per 1000 atoms: 0.52 Number of scatterers: 16443 At special positions: 0 Unit cell: (99.56, 105.848, 136.24, 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 2869 8.00 N 2556 7.00 C 10903 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.02 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: 6.33 Conformation dependent library (CDL) restraints added in 2.3 seconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3692 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 6 sheets defined 67.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 17 through 20 Processing helix chain 'A' and resid 23 through 48 Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 120 through 140 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 147 through 164 removed outlier: 3.668A 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 283 removed outlier: 3.840A pdb=" N PHE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 313 through 344 removed outlier: 4.383A pdb=" N THR A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 321 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA A 322 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 329 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 335 " --> pdb=" O TYR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 370 through 382 removed outlier: 3.527A pdb=" N TYR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.783A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'B' and resid 17 through 20 Processing helix chain 'B' and resid 23 through 49 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 120 through 140 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 147 through 164 removed outlier: 3.789A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 234 through 254 Processing helix chain 'B' and resid 259 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 315 through 343 removed outlier: 3.906A pdb=" N PHE B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 371 through 382 Processing helix chain 'B' and resid 384 through 393 removed outlier: 3.817A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 5.089A 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 17 through 20 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 140 Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 142 through 145 No H-bonds generated for 'chain 'C' and resid 142 through 145' Processing helix chain 'C' and resid 147 through 165 removed outlier: 3.690A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 234 through 254 Processing helix chain 'C' and resid 259 through 288 removed outlier: 4.748A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASN C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 343 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 370 through 382 removed outlier: 3.514A pdb=" N TYR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 393 removed outlier: 3.920A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 409 Processing helix chain 'D' and resid 17 through 20 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: 5.005A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 164 removed outlier: 3.905A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 234 through 254 Processing helix chain 'D' and resid 259 through 288 removed outlier: 4.670A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 5.616A 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: 4.009A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 406 Processing helix chain 'E' and resid 23 through 48 Processing helix chain 'E' and resid 103 through 116 Processing helix chain 'E' and resid 120 through 140 Proline residue: E 126 - end of helix Processing helix chain 'E' and resid 147 through 164 removed outlier: 3.766A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 234 through 254 Processing helix chain 'E' and resid 259 through 288 removed outlier: 4.800A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASN E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 342 Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 371 through 382 Processing helix chain 'E' and resid 384 through 393 removed outlier: 3.871A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 409 Processing helix chain 'F' and resid 18 through 20 No H-bonds generated for 'chain 'F' and resid 18 through 20' 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 167 removed outlier: 3.882A pdb=" N SER F 153 " --> pdb=" O PRO F 149 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) 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: 4.882A pdb=" N SER F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 342 Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 368 through 380 Processing helix chain 'F' and resid 382 through 392 removed outlier: 3.718A pdb=" N LYS F 386 " --> pdb=" O PRO F 382 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.129A 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 53 through 56 Processing sheet with id= E, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.556A pdb=" N LEU E 55 " --> pdb=" O ARG E 309 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 52 through 56 961 hydrogen bonds defined for protein. 2784 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: 4.41 Time building geometry restraints manager: 6.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2761 1.33 - 1.45: 4646 1.45 - 1.57: 9280 1.57 - 1.69: 10 1.69 - 1.81: 161 Bond restraints: 16858 Sorted by residual: bond pdb=" C10 PEE A 902 " pdb=" O4 PEE A 902 " ideal model delta sigma weight residual 1.206 1.358 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" C10 PEE E 902 " pdb=" O4 PEE E 902 " 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 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 5.72e+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 5.71e+01 bond pdb=" C10 PEE E 903 " pdb=" O4 PEE E 903 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 16853 not shown) Histogram of bond angle deviations from ideal: 90.55 - 99.29: 11 99.29 - 108.03: 634 108.03 - 116.78: 10564 116.78 - 125.52: 11165 125.52 - 134.26: 303 Bond angle restraints: 22677 Sorted by residual: angle pdb=" O1P PEE F 904 " pdb=" P PEE F 904 " pdb=" O2P PEE F 904 " ideal model delta sigma weight residual 119.43 133.28 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE D 901 " pdb=" P PEE D 901 " pdb=" O2P PEE D 901 " ideal model delta sigma weight residual 119.43 133.26 -13.83 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE D 904 " pdb=" P PEE D 904 " pdb=" O2P PEE D 904 " ideal model delta sigma weight residual 119.43 133.22 -13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.20 -13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.18 -13.75 3.00e+00 1.11e-01 2.10e+01 ... (remaining 22672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 9715 35.96 - 71.93: 316 71.93 - 107.89: 24 107.89 - 143.85: 14 143.85 - 179.82: 16 Dihedral angle restraints: 10085 sinusoidal: 4381 harmonic: 5704 Sorted by residual: dihedral pdb=" CB CYS B 113 " pdb=" SG CYS B 113 " pdb=" SG CYS B 295 " pdb=" CB CYS B 295 " ideal model delta sinusoidal sigma weight residual 93.00 50.48 42.52 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" N PEE A 901 " pdb=" C4 PEE A 901 " pdb=" C5 PEE A 901 " pdb=" O4P PEE A 901 " ideal model delta sinusoidal sigma weight residual -56.97 122.85 -179.82 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N PEE B 901 " pdb=" C4 PEE B 901 " pdb=" C5 PEE B 901 " pdb=" O4P PEE B 901 " ideal model delta sinusoidal sigma weight residual -56.97 119.91 -176.88 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 10082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2293 0.084 - 0.167: 132 0.167 - 0.251: 1 0.251 - 0.335: 0 0.335 - 0.418: 10 Chirality restraints: 2436 Sorted by residual: chirality pdb=" C2 PEE B 904 " pdb=" C1 PEE B 904 " pdb=" C3 PEE B 904 " pdb=" O2 PEE B 904 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.37e+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 4.22e+00 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 -2.74 0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 2433 not shown) Planarity restraints: 2714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 321 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C LEU D 321 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU D 321 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA D 322 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 244 " -0.013 2.00e-02 2.50e+03 1.82e-02 5.81e+00 pdb=" CG PHE A 244 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A 244 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 244 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 244 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 244 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 244 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 324 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C PHE D 324 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE D 324 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR D 325 " -0.013 2.00e-02 2.50e+03 ... (remaining 2711 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1658 2.75 - 3.29: 16418 3.29 - 3.82: 28959 3.82 - 4.36: 33293 4.36 - 4.90: 57731 Nonbonded interactions: 138059 Sorted by model distance: nonbonded pdb=" O SER E 395 " pdb=" OG SER E 398 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR E 99 " pdb=" O MET F 300 " model vdw 2.213 2.440 nonbonded pdb=" O SER A 166 " pdb=" OG1 THR A 169 " model vdw 2.232 2.440 nonbonded pdb=" O SER D 166 " pdb=" OG1 THR D 169 " model vdw 2.233 2.440 nonbonded pdb=" O SER B 166 " pdb=" OG1 THR B 169 " model vdw 2.233 2.440 ... (remaining 138054 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 407 or (resid 901 through 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O2 \ or name O4 )))) selection = (chain 'B' and (resid 15 through 407 or (resid 901 through 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O2 \ or name O4 )))) selection = (chain 'C' and (resid 15 through 407 or (resid 901 through 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O2 \ or name O4 )))) selection = (chain 'D' and (resid 15 through 407 or (resid 902 through 904 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O2 \ or name O4 )))) selection = (chain 'E' and (resid 15 through 407 or (resid 901 through 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O2 \ or name O4 )))) } 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 15.760 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 41.390 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.006 0.152 16858 Z= 0.400 Angle : 0.839 13.848 22677 Z= 0.403 Chirality : 0.048 0.418 2436 Planarity : 0.005 0.056 2714 Dihedral : 19.554 179.817 6342 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.28 % Allowed : 16.62 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.19), residues: 1865 helix: 1.11 (0.14), residues: 1276 sheet: 0.24 (0.52), residues: 104 loop : -0.72 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 168 HIS 0.009 0.001 HIS C 253 PHE 0.037 0.002 PHE A 244 TYR 0.018 0.001 TYR B 281 ARG 0.009 0.001 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 338 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.7947 (tp30) cc_final: 0.7364 (tp30) REVERT: A 258 ASP cc_start: 0.8320 (p0) cc_final: 0.7905 (p0) REVERT: B 245 GLU cc_start: 0.7589 (tp30) cc_final: 0.7232 (tp30) REVERT: B 248 LYS cc_start: 0.8311 (mppt) cc_final: 0.8007 (mmtp) REVERT: C 29 ASP cc_start: 0.7859 (t0) cc_final: 0.7526 (t0) REVERT: D 244 PHE cc_start: 0.5627 (m-80) cc_final: 0.5157 (t80) REVERT: D 250 PHE cc_start: 0.7249 (t80) cc_final: 0.7045 (t80) REVERT: E 375 MET cc_start: 0.7691 (mtm) cc_final: 0.7326 (mtp) REVERT: E 393 PHE cc_start: 0.5975 (m-80) cc_final: 0.5181 (m-80) REVERT: F 148 PHE cc_start: 0.6999 (t80) cc_final: 0.6370 (t80) REVERT: F 154 LYS cc_start: 0.7786 (mttt) cc_final: 0.6946 (mmpt) REVERT: F 170 TRP cc_start: 0.6076 (t-100) cc_final: 0.5297 (t-100) REVERT: F 367 LYS cc_start: 0.7639 (ptmt) cc_final: 0.7158 (mttp) REVERT: F 386 LYS cc_start: 0.8400 (mtpp) cc_final: 0.8118 (mmtt) outliers start: 5 outliers final: 0 residues processed: 342 average time/residue: 1.1365 time to fit residues: 436.6811 Evaluate side-chains 221 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 408 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS E 409 ASN F 60 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 HIS F 305 ASN F 309 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16858 Z= 0.286 Angle : 0.517 8.780 22677 Z= 0.271 Chirality : 0.039 0.187 2436 Planarity : 0.003 0.048 2714 Dihedral : 16.537 169.848 2542 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.37 % Allowed : 19.23 % Favored : 76.40 % 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: 1.69 (0.19), residues: 1865 helix: 1.83 (0.14), residues: 1275 sheet: 0.53 (0.52), residues: 108 loop : -0.60 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 168 HIS 0.006 0.001 HIS F 251 PHE 0.016 0.002 PHE B 353 TYR 0.018 0.002 TYR C 281 ARG 0.004 0.000 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 240 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 ASP cc_start: 0.8295 (p0) cc_final: 0.7819 (p0) REVERT: A 275 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8478 (t80) REVERT: B 245 GLU cc_start: 0.7608 (tp30) cc_final: 0.7326 (tp30) REVERT: B 372 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.8066 (t80) REVERT: C 29 ASP cc_start: 0.7848 (t0) cc_final: 0.7494 (t0) REVERT: C 168 TRP cc_start: 0.7845 (t-100) cc_final: 0.7575 (t-100) REVERT: C 280 CYS cc_start: 0.8722 (m) cc_final: 0.8450 (m) REVERT: C 352 SER cc_start: 0.8135 (OUTLIER) cc_final: 0.7913 (p) REVERT: D 59 TRP cc_start: 0.7211 (m-10) cc_final: 0.6986 (m100) REVERT: D 244 PHE cc_start: 0.5679 (m-80) cc_final: 0.5270 (t80) REVERT: D 353 PHE cc_start: 0.6276 (m-80) cc_final: 0.6019 (m-80) REVERT: E 164 PHE cc_start: 0.7151 (t80) cc_final: 0.6841 (t80) REVERT: E 243 LEU cc_start: 0.7775 (tt) cc_final: 0.7433 (mt) REVERT: E 254 VAL cc_start: 0.6157 (OUTLIER) cc_final: 0.5954 (p) REVERT: E 371 ASP cc_start: 0.7588 (t0) cc_final: 0.7364 (t0) REVERT: F 58 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7669 (mtm110) REVERT: F 96 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7823 (mtp) REVERT: F 146 PHE cc_start: 0.7634 (m-10) cc_final: 0.7387 (m-80) REVERT: F 170 TRP cc_start: 0.6352 (t-100) cc_final: 0.5676 (t-100) REVERT: F 346 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7015 (tt) REVERT: F 367 LYS cc_start: 0.7967 (ptmt) cc_final: 0.7560 (ptpp) REVERT: F 386 LYS cc_start: 0.8324 (mtpp) cc_final: 0.8013 (mmtt) outliers start: 77 outliers final: 23 residues processed: 286 average time/residue: 0.9178 time to fit residues: 302.4274 Evaluate side-chains 246 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 346 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 chunk 181 optimal weight: 0.0970 chunk 149 optimal weight: 0.0470 chunk 166 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.5876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN D 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16858 Z= 0.168 Angle : 0.449 8.452 22677 Z= 0.236 Chirality : 0.037 0.160 2436 Planarity : 0.003 0.043 2714 Dihedral : 14.137 176.578 2542 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.80 % Allowed : 20.42 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.19), residues: 1865 helix: 1.93 (0.14), residues: 1310 sheet: 0.89 (0.53), residues: 108 loop : -0.84 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 24 HIS 0.004 0.001 HIS B 253 PHE 0.017 0.001 PHE D 144 TYR 0.014 0.001 TYR D 338 ARG 0.004 0.000 ARG F 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 245 time to evaluate : 1.928 Fit side-chains revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8610 (OUTLIER) cc_final: 0.8274 (m-70) REVERT: A 115 GLU cc_start: 0.8061 (tp30) cc_final: 0.7468 (tp30) REVERT: A 258 ASP cc_start: 0.8202 (p0) cc_final: 0.7855 (p0) REVERT: B 162 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7079 (mptt) REVERT: B 245 GLU cc_start: 0.7584 (tp30) cc_final: 0.7243 (tp30) REVERT: C 29 ASP cc_start: 0.7837 (t0) cc_final: 0.7318 (t0) REVERT: C 33 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8366 (mp) REVERT: C 168 TRP cc_start: 0.7859 (t-100) cc_final: 0.7611 (t-100) REVERT: D 244 PHE cc_start: 0.5735 (m-80) cc_final: 0.5310 (t80) REVERT: D 353 PHE cc_start: 0.6328 (m-80) cc_final: 0.6063 (m-80) REVERT: E 164 PHE cc_start: 0.7323 (t80) cc_final: 0.7034 (t80) REVERT: E 254 VAL cc_start: 0.6288 (OUTLIER) cc_final: 0.6033 (p) REVERT: E 255 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6681 (tp30) REVERT: E 375 MET cc_start: 0.7546 (mtm) cc_final: 0.7276 (mtm) REVERT: E 390 PHE cc_start: 0.8356 (t80) cc_final: 0.8135 (t80) REVERT: F 58 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7691 (mtm110) REVERT: F 96 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7774 (mtp) REVERT: F 146 PHE cc_start: 0.7492 (m-10) cc_final: 0.7269 (m-80) REVERT: F 170 TRP cc_start: 0.6312 (t-100) cc_final: 0.5741 (t-100) REVERT: F 348 GLU cc_start: 0.7750 (pp20) cc_final: 0.7472 (tp30) REVERT: F 367 LYS cc_start: 0.8192 (ptmt) cc_final: 0.7463 (ptpp) REVERT: F 386 LYS cc_start: 0.8335 (mtpp) cc_final: 0.8041 (mmtt) REVERT: F 388 PHE cc_start: 0.5910 (t80) cc_final: 0.5351 (t80) outliers start: 67 outliers final: 26 residues processed: 292 average time/residue: 0.8702 time to fit residues: 293.6535 Evaluate side-chains 247 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS F 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16858 Z= 0.235 Angle : 0.473 8.895 22677 Z= 0.249 Chirality : 0.038 0.140 2436 Planarity : 0.003 0.041 2714 Dihedral : 13.144 168.015 2542 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.76 % Allowed : 20.82 % Favored : 74.42 % 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: 2.12 (0.20), residues: 1865 helix: 2.14 (0.14), residues: 1279 sheet: 0.94 (0.54), residues: 108 loop : -0.51 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 168 HIS 0.004 0.001 HIS B 253 PHE 0.028 0.001 PHE D 250 TYR 0.019 0.001 TYR C 281 ARG 0.004 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 215 time to evaluate : 1.721 Fit side-chains revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8605 (OUTLIER) cc_final: 0.8273 (m-70) REVERT: A 115 GLU cc_start: 0.8082 (tp30) cc_final: 0.7562 (tp30) REVERT: A 245 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7551 (mm-30) REVERT: A 258 ASP cc_start: 0.8264 (p0) cc_final: 0.7905 (p0) REVERT: A 275 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8433 (t80) REVERT: B 18 ARG cc_start: 0.8439 (ptm-80) cc_final: 0.8162 (ptt180) REVERT: B 162 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7120 (mptt) REVERT: B 245 GLU cc_start: 0.7597 (tp30) cc_final: 0.7247 (tp30) REVERT: B 365 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6537 (mm) REVERT: C 29 ASP cc_start: 0.7848 (t0) cc_final: 0.7518 (t0) REVERT: D 244 PHE cc_start: 0.5640 (OUTLIER) cc_final: 0.5226 (t80) REVERT: D 353 PHE cc_start: 0.6385 (m-80) cc_final: 0.6106 (m-80) REVERT: D 405 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5877 (pp) REVERT: E 164 PHE cc_start: 0.7256 (t80) cc_final: 0.7004 (t80) REVERT: E 275 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7864 (t80) REVERT: E 306 ARG cc_start: 0.7559 (mtm110) cc_final: 0.7329 (ttp-110) REVERT: E 390 PHE cc_start: 0.8353 (t80) cc_final: 0.8066 (t80) REVERT: F 96 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7847 (mtp) REVERT: F 146 PHE cc_start: 0.7551 (m-10) cc_final: 0.7326 (m-80) REVERT: F 170 TRP cc_start: 0.6391 (t-100) cc_final: 0.5914 (t-100) REVERT: F 367 LYS cc_start: 0.8134 (ptmt) cc_final: 0.7681 (ptpp) REVERT: F 386 LYS cc_start: 0.8418 (mtpp) cc_final: 0.8131 (mmtt) REVERT: F 388 PHE cc_start: 0.6355 (t80) cc_final: 0.6005 (t80) outliers start: 84 outliers final: 37 residues processed: 273 average time/residue: 0.9191 time to fit residues: 289.5722 Evaluate side-chains 248 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 203 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN F 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16858 Z= 0.210 Angle : 0.458 9.104 22677 Z= 0.242 Chirality : 0.038 0.147 2436 Planarity : 0.003 0.038 2714 Dihedral : 11.840 155.948 2542 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.20 % Allowed : 22.06 % Favored : 73.74 % 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: 2.17 (0.19), residues: 1865 helix: 2.18 (0.14), residues: 1278 sheet: 0.84 (0.53), residues: 110 loop : -0.48 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 168 HIS 0.005 0.001 HIS B 253 PHE 0.029 0.001 PHE D 250 TYR 0.015 0.001 TYR C 281 ARG 0.004 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 215 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8637 (OUTLIER) cc_final: 0.8221 (m-70) REVERT: A 115 GLU cc_start: 0.8016 (tp30) cc_final: 0.7553 (tp30) REVERT: A 245 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7731 (mm-30) REVERT: A 258 ASP cc_start: 0.8291 (p0) cc_final: 0.7942 (p0) REVERT: A 275 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8444 (t80) REVERT: B 18 ARG cc_start: 0.8476 (ptm-80) cc_final: 0.8206 (ptt180) REVERT: B 162 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7205 (mmpt) REVERT: B 245 GLU cc_start: 0.7602 (tp30) cc_final: 0.7249 (tp30) REVERT: B 365 ILE cc_start: 0.6786 (OUTLIER) cc_final: 0.6575 (mm) REVERT: C 29 ASP cc_start: 0.7786 (t0) cc_final: 0.7262 (t0) REVERT: C 168 TRP cc_start: 0.7926 (t-100) cc_final: 0.7590 (t-100) REVERT: C 245 GLU cc_start: 0.7242 (tp30) cc_final: 0.6895 (tp30) REVERT: D 244 PHE cc_start: 0.5770 (OUTLIER) cc_final: 0.5362 (t80) REVERT: D 405 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5852 (pp) REVERT: E 164 PHE cc_start: 0.7115 (t80) cc_final: 0.6826 (t80) REVERT: E 250 PHE cc_start: 0.6572 (t80) cc_final: 0.6324 (t80) REVERT: E 275 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7467 (t80) REVERT: E 306 ARG cc_start: 0.7514 (mtm110) cc_final: 0.7229 (ttp-110) REVERT: E 390 PHE cc_start: 0.8315 (t80) cc_final: 0.7932 (t80) REVERT: F 18 ARG cc_start: 0.8453 (ttp-110) cc_final: 0.8037 (ttt-90) REVERT: F 96 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7823 (mtp) REVERT: F 146 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7491 (m-80) REVERT: F 170 TRP cc_start: 0.6490 (t-100) cc_final: 0.6048 (t-100) REVERT: F 348 GLU cc_start: 0.7883 (pp20) cc_final: 0.7649 (tp30) REVERT: F 349 TYR cc_start: 0.6549 (t80) cc_final: 0.5832 (t80) REVERT: F 386 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8152 (mmtt) REVERT: F 388 PHE cc_start: 0.6243 (t80) cc_final: 0.5694 (t80) outliers start: 74 outliers final: 38 residues processed: 267 average time/residue: 0.8977 time to fit residues: 277.0806 Evaluate side-chains 251 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 204 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 146 PHE Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.7980 chunk 161 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 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 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS A 404 GLN A 408 ASN D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16858 Z= 0.171 Angle : 0.448 9.600 22677 Z= 0.235 Chirality : 0.037 0.150 2436 Planarity : 0.003 0.036 2714 Dihedral : 11.097 140.914 2542 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.48 % Allowed : 22.06 % Favored : 73.45 % 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: 2.18 (0.20), residues: 1865 helix: 2.18 (0.14), residues: 1290 sheet: 0.89 (0.53), residues: 110 loop : -0.52 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 341 HIS 0.004 0.001 HIS B 253 PHE 0.031 0.001 PHE D 250 TYR 0.013 0.001 TYR C 281 ARG 0.002 0.000 ARG F 249 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 218 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8195 (m-80) cc_final: 0.7964 (m-80) REVERT: A 104 HIS cc_start: 0.8545 (OUTLIER) cc_final: 0.8247 (m-70) REVERT: A 245 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7705 (mm-30) REVERT: A 258 ASP cc_start: 0.8285 (p0) cc_final: 0.7999 (p0) REVERT: A 275 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8440 (t80) REVERT: B 18 ARG cc_start: 0.8432 (ptm-80) cc_final: 0.8157 (ptt180) REVERT: B 162 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7132 (mmpt) REVERT: B 245 GLU cc_start: 0.7519 (tp30) cc_final: 0.7165 (tp30) REVERT: B 385 LEU cc_start: 0.8309 (tt) cc_final: 0.8048 (tm) REVERT: C 29 ASP cc_start: 0.7810 (t0) cc_final: 0.7222 (t0) REVERT: C 33 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8446 (mp) REVERT: C 160 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7198 (tp) REVERT: C 168 TRP cc_start: 0.7905 (t-100) cc_final: 0.7583 (t-100) REVERT: C 245 GLU cc_start: 0.7243 (tp30) cc_final: 0.6887 (tp30) REVERT: D 244 PHE cc_start: 0.5738 (OUTLIER) cc_final: 0.5287 (t80) REVERT: D 309 ARG cc_start: 0.8093 (tpp-160) cc_final: 0.7828 (ttm-80) REVERT: D 375 MET cc_start: 0.7925 (mtm) cc_final: 0.7663 (mpp) REVERT: D 405 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5910 (pp) REVERT: E 164 PHE cc_start: 0.7120 (t80) cc_final: 0.6878 (t80) REVERT: E 266 ARG cc_start: 0.7846 (mpt-90) cc_final: 0.7631 (mmt90) REVERT: E 275 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7430 (t80) REVERT: E 306 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7221 (ttp-110) REVERT: E 390 PHE cc_start: 0.8347 (t80) cc_final: 0.7922 (t80) REVERT: F 18 ARG cc_start: 0.8470 (ttp-110) cc_final: 0.8060 (ttt-90) REVERT: F 96 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7797 (mtp) REVERT: F 170 TRP cc_start: 0.6562 (t-100) cc_final: 0.6185 (t-100) REVERT: F 348 GLU cc_start: 0.7934 (pp20) cc_final: 0.7644 (tp30) REVERT: F 370 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6064 (t80) REVERT: F 386 LYS cc_start: 0.8371 (mtpp) cc_final: 0.8142 (mmtt) REVERT: F 388 PHE cc_start: 0.6016 (t80) cc_final: 0.5642 (t80) outliers start: 79 outliers final: 41 residues processed: 273 average time/residue: 0.8971 time to fit residues: 283.5192 Evaluate side-chains 259 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 208 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 250 PHE Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN F 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16858 Z= 0.217 Angle : 0.469 9.545 22677 Z= 0.247 Chirality : 0.038 0.155 2436 Planarity : 0.003 0.035 2714 Dihedral : 10.777 141.174 2542 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.37 % Allowed : 22.40 % Favored : 73.23 % 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: 2.26 (0.19), residues: 1865 helix: 2.23 (0.14), residues: 1278 sheet: 0.82 (0.53), residues: 110 loop : -0.36 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 341 HIS 0.004 0.001 HIS B 253 PHE 0.033 0.001 PHE D 250 TYR 0.016 0.001 TYR C 281 ARG 0.003 0.000 ARG F 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 209 time to evaluate : 1.801 Fit side-chains revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8151 (m-80) cc_final: 0.7899 (m-80) REVERT: A 104 HIS cc_start: 0.8576 (OUTLIER) cc_final: 0.8256 (m-70) REVERT: A 258 ASP cc_start: 0.8238 (p0) cc_final: 0.7943 (p0) REVERT: A 275 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8453 (t80) REVERT: B 18 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8185 (ptt180) REVERT: B 162 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7158 (mmpt) REVERT: B 245 GLU cc_start: 0.7545 (tp30) cc_final: 0.7178 (tp30) REVERT: C 29 ASP cc_start: 0.7807 (t0) cc_final: 0.7227 (t0) REVERT: C 160 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7113 (tp) REVERT: C 168 TRP cc_start: 0.7724 (t-100) cc_final: 0.7511 (t-100) REVERT: D 244 PHE cc_start: 0.5821 (OUTLIER) cc_final: 0.5396 (t80) REVERT: D 354 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: D 405 LEU cc_start: 0.6246 (OUTLIER) cc_final: 0.5921 (pp) REVERT: E 164 PHE cc_start: 0.7148 (t80) cc_final: 0.6918 (t80) REVERT: E 266 ARG cc_start: 0.7906 (mpt-90) cc_final: 0.7679 (mmt90) REVERT: E 275 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7748 (t80) REVERT: E 306 ARG cc_start: 0.7519 (mtm110) cc_final: 0.7280 (ttp-110) REVERT: E 390 PHE cc_start: 0.8383 (t80) cc_final: 0.7943 (t80) REVERT: F 18 ARG cc_start: 0.8553 (ttp-110) cc_final: 0.8284 (ttt-90) REVERT: F 96 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7835 (mtp) REVERT: F 348 GLU cc_start: 0.8036 (pp20) cc_final: 0.7707 (tp30) REVERT: F 357 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6605 (mp0) REVERT: F 370 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6045 (t80) REVERT: F 386 LYS cc_start: 0.8361 (mtpp) cc_final: 0.8022 (mmtt) REVERT: F 388 PHE cc_start: 0.6136 (t80) cc_final: 0.5666 (t80) outliers start: 77 outliers final: 45 residues processed: 260 average time/residue: 0.8692 time to fit residues: 262.2347 Evaluate side-chains 253 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 197 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 104 HIS 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 314 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN F 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16858 Z= 0.215 Angle : 0.479 9.848 22677 Z= 0.251 Chirality : 0.038 0.157 2436 Planarity : 0.003 0.035 2714 Dihedral : 10.305 140.124 2542 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.03 % Allowed : 22.97 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.20), residues: 1865 helix: 2.18 (0.14), residues: 1279 sheet: 0.79 (0.53), residues: 110 loop : -0.34 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 170 HIS 0.004 0.001 HIS B 253 PHE 0.034 0.001 PHE D 250 TYR 0.015 0.001 TYR C 281 ARG 0.002 0.000 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 207 time to evaluate : 1.798 Fit side-chains revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8194 (m-80) cc_final: 0.7941 (m-80) REVERT: A 104 HIS cc_start: 0.8637 (OUTLIER) cc_final: 0.8218 (m-70) REVERT: A 258 ASP cc_start: 0.8246 (p0) cc_final: 0.7928 (p0) REVERT: B 18 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8274 (ptt180) REVERT: B 162 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7278 (mmpt) REVERT: B 245 GLU cc_start: 0.7539 (tp30) cc_final: 0.7162 (tp30) REVERT: B 385 LEU cc_start: 0.8314 (tt) cc_final: 0.8053 (tm) REVERT: B 405 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6815 (mp) REVERT: C 29 ASP cc_start: 0.7714 (t0) cc_final: 0.7324 (t0) REVERT: C 160 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7125 (tp) REVERT: D 244 PHE cc_start: 0.5640 (OUTLIER) cc_final: 0.5249 (t80) REVERT: D 354 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6452 (mp0) REVERT: D 405 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5907 (pp) REVERT: E 164 PHE cc_start: 0.7077 (t80) cc_final: 0.6854 (t80) REVERT: E 266 ARG cc_start: 0.7918 (mpt-90) cc_final: 0.7685 (mmt90) REVERT: E 275 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7652 (t80) REVERT: E 306 ARG cc_start: 0.7520 (mtm110) cc_final: 0.7305 (ttp-110) REVERT: E 390 PHE cc_start: 0.8450 (t80) cc_final: 0.8004 (t80) REVERT: F 18 ARG cc_start: 0.8601 (ttp-110) cc_final: 0.8325 (ttt-90) REVERT: F 96 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7836 (mtp) REVERT: F 357 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6746 (mp0) REVERT: F 370 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6005 (t80) REVERT: F 386 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8071 (mmtt) REVERT: F 388 PHE cc_start: 0.6168 (t80) cc_final: 0.5700 (t80) outliers start: 71 outliers final: 48 residues processed: 258 average time/residue: 0.8424 time to fit residues: 253.7147 Evaluate side-chains 261 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 202 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 370 PHE Chi-restraints excluded: chain F residue 377 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.4981 > 50: distance: 29 - 36: 9.448 distance: 36 - 37: 5.966 distance: 37 - 38: 28.467 distance: 37 - 40: 24.318 distance: 38 - 39: 13.710 distance: 38 - 45: 56.069 distance: 40 - 41: 13.833 distance: 41 - 42: 14.579 distance: 42 - 43: 16.363 distance: 43 - 44: 42.315 distance: 45 - 46: 23.035 distance: 46 - 47: 23.279 distance: 46 - 49: 9.470 distance: 47 - 48: 23.438 distance: 47 - 56: 25.287 distance: 49 - 50: 15.033 distance: 50 - 51: 12.191 distance: 50 - 52: 16.563 distance: 51 - 53: 20.310 distance: 52 - 54: 14.095 distance: 53 - 55: 15.525 distance: 54 - 55: 9.719 distance: 56 - 57: 23.226 distance: 56 - 62: 25.338 distance: 57 - 58: 22.639 distance: 57 - 60: 21.122 distance: 58 - 59: 18.364 distance: 58 - 63: 12.048 distance: 60 - 61: 6.407 distance: 61 - 62: 22.711 distance: 63 - 64: 15.198 distance: 64 - 65: 6.973 distance: 65 - 66: 10.010 distance: 65 - 67: 8.487 distance: 67 - 68: 5.392 distance: 68 - 69: 14.968 distance: 68 - 71: 15.105 distance: 69 - 70: 11.488 distance: 69 - 73: 26.097 distance: 70 - 94: 23.213 distance: 71 - 72: 7.060 distance: 73 - 74: 7.864 distance: 74 - 75: 5.347 distance: 74 - 77: 11.614 distance: 75 - 76: 5.300 distance: 75 - 79: 6.835 distance: 76 - 102: 21.603 distance: 77 - 78: 4.270 distance: 79 - 80: 8.129 distance: 80 - 81: 10.570 distance: 80 - 83: 14.297 distance: 81 - 82: 35.876 distance: 81 - 85: 4.586 distance: 82 - 111: 34.490 distance: 83 - 84: 10.821 distance: 85 - 86: 4.292 distance: 86 - 87: 21.161 distance: 86 - 89: 22.859 distance: 87 - 94: 23.530 distance: 88 - 118: 18.992 distance: 89 - 90: 11.039 distance: 90 - 91: 13.444 distance: 91 - 92: 18.738 distance: 92 - 93: 7.788 distance: 94 - 95: 9.653 distance: 95 - 96: 14.101 distance: 95 - 98: 22.340 distance: 96 - 97: 9.436 distance: 96 - 102: 23.286 distance: 97 - 125: 24.749 distance: 98 - 99: 17.576 distance: 98 - 100: 9.823 distance: 99 - 101: 33.470 distance: 102 - 103: 13.048 distance: 103 - 104: 10.942 distance: 103 - 106: 10.682 distance: 104 - 105: 10.831 distance: 104 - 111: 15.327 distance: 105 - 133: 23.734 distance: 106 - 107: 4.477 distance: 107 - 108: 9.478 distance: 108 - 109: 15.729 distance: 108 - 110: 12.737