Starting phenix.real_space_refine on Mon Feb 19 20:26:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f77_28897/02_2024/8f77_28897_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f77_28897/02_2024/8f77_28897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f77_28897/02_2024/8f77_28897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f77_28897/02_2024/8f77_28897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f77_28897/02_2024/8f77_28897_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f77_28897/02_2024/8f77_28897_updated.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 138 5.16 5 C 16811 2.51 5 N 4191 2.21 5 O 4534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 29": "OD1" <-> "OD2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A ASP 165": "OD1" <-> "OD2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 703": "OD1" <-> "OD2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B ASP 380": "OD1" <-> "OD2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 29": "OD1" <-> "OD2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 367": "OD1" <-> "OD2" Residue "E PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ASP 104": "OD1" <-> "OD2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "F PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 296": "OD1" <-> "OD2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 595": "OE1" <-> "OE2" Residue "F GLU 628": "OE1" <-> "OE2" Residue "F PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 795": "OD1" <-> "OD2" Residue "F GLU 798": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25678 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5916 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "B" Number of atoms: 5912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5912 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 27, 'TRANS': 688} Chain breaks: 2 Chain: "C" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2560 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain breaks: 2 Chain: "D" Number of atoms: 2637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2637 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 9, 'TRANS': 304} Chain breaks: 2 Chain: "E" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2652 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "F" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5751 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 24, 'TRANS': 679} Chain breaks: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 13.78, per 1000 atoms: 0.54 Number of scatterers: 25678 At special positions: 0 Unit cell: (128.904, 126.808, 197.024, 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 138 16.00 P 4 15.00 O 4534 8.00 N 4191 7.00 C 16811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.42 Conformation dependent library (CDL) restraints added in 4.6 seconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5970 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 131 helices and 14 sheets defined 51.8% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.83 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 removed outlier: 4.098A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 49 Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 120 through 140 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 142 through 145 No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 147 through 164 removed outlier: 4.141A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 234 through 254 Processing helix chain 'A' and resid 259 through 284 removed outlier: 3.972A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 313 through 345 removed outlier: 4.293A pdb=" N THR A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG A 345 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 370 through 382 Processing helix chain 'A' and resid 384 through 394 removed outlier: 4.202A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 440 through 443 No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 463 through 466 Processing helix chain 'A' and resid 485 through 494 Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.627A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 586 through 589 removed outlier: 4.032A pdb=" N LYS A 589 " --> pdb=" O SER A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 586 through 589' Processing helix chain 'A' and resid 609 through 612 No H-bonds generated for 'chain 'A' and resid 609 through 612' Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.954A pdb=" N ILE A 633 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 796 through 807 Processing helix chain 'B' and resid 16 through 20 removed outlier: 4.149A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 49 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 120 through 145 Proline residue: B 126 - end of helix removed outlier: 4.604A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 165 Processing helix chain 'B' and resid 167 through 174 removed outlier: 3.537A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 254 Processing helix chain 'B' and resid 259 through 288 removed outlier: 5.051A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASN B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 342 Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 370 through 382 Processing helix chain 'B' and resid 384 through 393 removed outlier: 4.381A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 410 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 441 through 444 No H-bonds generated for 'chain 'B' and resid 441 through 444' Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 485 through 494 removed outlier: 3.648A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 507 removed outlier: 3.877A pdb=" N GLU B 507 " --> pdb=" O ASP B 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 504 through 507' Processing helix chain 'B' and resid 560 through 568 removed outlier: 4.712A pdb=" N VAL B 567 " --> pdb=" O THR B 563 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N HIS B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 634 through 637 removed outlier: 3.757A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 637' Processing helix chain 'B' and resid 656 through 660 Processing helix chain 'B' and resid 680 through 683 Processing helix chain 'B' and resid 702 through 704 No H-bonds generated for 'chain 'B' and resid 702 through 704' Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 748 through 751 Processing helix chain 'B' and resid 771 through 775 Processing helix chain 'B' and resid 788 through 793 removed outlier: 4.063A pdb=" N THR B 793 " --> pdb=" O ASP B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 807 Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 23 through 49 removed outlier: 3.603A pdb=" N MET C 37 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 116 Processing helix chain 'C' and resid 120 through 145 Proline residue: C 126 - end of helix removed outlier: 4.657A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 164 Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 236 through 254 Processing helix chain 'C' and resid 259 through 288 removed outlier: 4.895A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASN C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 343 removed outlier: 4.272A pdb=" N THR C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU C 317 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 370 through 382 Processing helix chain 'C' and resid 384 through 390 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'D' and resid 16 through 20 removed outlier: 4.282A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 48 Processing helix chain 'D' and resid 103 through 116 Processing helix chain 'D' and resid 120 through 143 Proline residue: D 126 - end of helix removed outlier: 4.842A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 164 Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 234 through 255 Processing helix chain 'D' and resid 259 through 288 removed outlier: 4.929A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASN D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 345 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 371 through 382 Processing helix chain 'D' and resid 384 through 393 removed outlier: 4.016A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 407 Processing helix chain 'E' and resid 18 through 20 No H-bonds generated for 'chain 'E' and resid 18 through 20' Processing helix chain 'E' and resid 23 through 49 Processing helix chain 'E' and resid 103 through 116 Processing helix chain 'E' and resid 120 through 145 Proline residue: E 126 - end of helix removed outlier: 4.643A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 165 removed outlier: 4.163A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 234 through 254 Processing helix chain 'E' and resid 259 through 288 removed outlier: 5.125A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASN E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 344 removed outlier: 3.553A pdb=" N LEU E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 370 through 382 Processing helix chain 'E' and resid 384 through 393 removed outlier: 3.964A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 408 Processing helix chain 'F' and resid 23 through 48 Processing helix chain 'F' and resid 105 through 118 removed outlier: 3.525A pdb=" N ARG F 118 " --> pdb=" O MET F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 142 Proline residue: F 128 - end of helix Processing helix chain 'F' and resid 144 through 147 No H-bonds generated for 'chain 'F' and resid 144 through 147' Processing helix chain 'F' and resid 149 through 167 Processing helix chain 'F' and resid 169 through 178 Processing helix chain 'F' and resid 233 through 252 Processing helix chain 'F' and resid 258 through 283 Processing helix chain 'F' and resid 298 through 301 No H-bonds generated for 'chain 'F' and resid 298 through 301' Processing helix chain 'F' and resid 313 through 343 Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 369 through 388 Proline residue: F 382 - end of helix removed outlier: 4.016A pdb=" N SER F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 408 Processing helix chain 'F' and resid 411 through 417 Processing helix chain 'F' and resid 461 through 465 Processing helix chain 'F' and resid 483 through 492 Processing helix chain 'F' and resid 503 through 505 No H-bonds generated for 'chain 'F' and resid 503 through 505' Processing helix chain 'F' and resid 509 through 512 Processing helix chain 'F' and resid 535 through 539 removed outlier: 4.042A pdb=" N ARG F 539 " --> pdb=" O GLU F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 563 Processing helix chain 'F' and resid 582 through 587 Processing helix chain 'F' and resid 606 through 610 Processing helix chain 'F' and resid 630 through 635 removed outlier: 4.564A pdb=" N GLN F 634 " --> pdb=" O VAL F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 658 Processing helix chain 'F' and resid 677 through 681 Processing helix chain 'F' and resid 700 through 704 removed outlier: 4.001A pdb=" N GLY F 703 " --> pdb=" O PRO F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 727 No H-bonds generated for 'chain 'F' and resid 724 through 727' Processing helix chain 'F' and resid 769 through 773 Processing helix chain 'F' and resid 786 through 790 Processing helix chain 'F' and resid 794 through 801 removed outlier: 3.838A pdb=" N MET F 800 " --> pdb=" O VAL F 796 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= B, first strand: chain 'A' and resid 429 through 433 removed outlier: 6.810A pdb=" N VAL A 450 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU A 432 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS A 452 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU A 473 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU A 453 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TRP A 475 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA A 497 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU A 476 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS A 499 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU A 520 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE A 500 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS A 522 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL A 548 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU A 523 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ARG A 550 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS A 571 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU A 551 " --> pdb=" O LYS A 571 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER A 573 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLU A 595 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ILE A 574 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU A 597 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU A 618 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU A 598 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASP A 620 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N CYS A 643 " --> pdb=" O ILE A 619 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 459 through 461 Processing sheet with id= D, first strand: chain 'A' and resid 666 through 668 removed outlier: 6.567A pdb=" N TYR A 689 " --> pdb=" O LEU A 667 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.557A pdb=" N ILE B 53 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 429 through 433 removed outlier: 7.556A pdb=" N VAL B 450 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU B 432 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS B 452 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLU B 473 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU B 453 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP B 475 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ALA B 497 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU B 476 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N HIS B 499 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU B 520 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ILE B 500 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS B 522 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL B 548 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU B 523 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG B 550 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LYS B 571 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B 551 " --> pdb=" O LYS B 571 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER B 573 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU B 595 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE B 574 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU B 597 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU B 618 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU B 598 " --> pdb=" O GLU B 618 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP B 620 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N CYS B 643 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ARG B 666 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR B 689 " --> pdb=" O LEU B 667 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 459 through 461 Processing sheet with id= H, first strand: chain 'B' and resid 712 through 714 removed outlier: 6.748A pdb=" N ALA B 735 " --> pdb=" O LEU B 713 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN B 758 " --> pdb=" O LEU B 736 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 52 through 56 Processing sheet with id= J, first strand: chain 'D' and resid 53 through 56 Processing sheet with id= K, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.749A pdb=" N ILE E 53 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 52 through 56 Processing sheet with id= M, first strand: chain 'F' and resid 427 through 431 removed outlier: 7.313A pdb=" N SER F 448 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU F 430 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LYS F 450 " --> pdb=" O LEU F 430 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLU F 471 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N LEU F 451 " --> pdb=" O GLU F 471 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS F 473 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL F 495 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LEU F 474 " --> pdb=" O VAL F 495 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER F 497 " --> pdb=" O LEU F 474 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU F 518 " --> pdb=" O LEU F 496 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL F 498 " --> pdb=" O GLU F 518 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR F 520 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE F 546 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS F 569 " --> pdb=" O LEU F 547 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE F 549 " --> pdb=" O LYS F 569 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N CYS F 571 " --> pdb=" O ILE F 549 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU F 593 " --> pdb=" O MET F 570 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL F 572 " --> pdb=" O GLU F 593 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU F 595 " --> pdb=" O VAL F 572 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLU F 616 " --> pdb=" O LEU F 594 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU F 596 " --> pdb=" O GLU F 616 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP F 618 " --> pdb=" O LEU F 596 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL F 641 " --> pdb=" O LEU F 617 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ARG F 664 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR F 687 " --> pdb=" O LEU F 665 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR F 710 " --> pdb=" O LEU F 688 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR F 733 " --> pdb=" O PHE F 711 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TYR F 756 " --> pdb=" O LEU F 734 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'F' and resid 457 through 459 1078 hydrogen bonds defined for protein. 2958 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: 8.58 Time building geometry restraints manager: 10.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4354 1.32 - 1.45: 6837 1.45 - 1.57: 14878 1.57 - 1.69: 6 1.69 - 1.81: 199 Bond restraints: 26274 Sorted by residual: bond pdb=" C10 PEE D 901 " pdb=" O4 PEE D 901 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C10 PEE B 903 " pdb=" O4 PEE B 903 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" O4P PEE A 901 " pdb=" P PEE A 901 " ideal model delta sigma weight residual 1.653 1.779 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" O4P PEE C 901 " pdb=" P PEE C 901 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" O4P PEE B 901 " pdb=" P PEE B 901 " ideal model delta sigma weight residual 1.653 1.775 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 26269 not shown) Histogram of bond angle deviations from ideal: 90.79 - 99.50: 6 99.50 - 108.22: 1065 108.22 - 116.93: 17207 116.93 - 125.65: 16788 125.65 - 134.36: 442 Bond angle restraints: 35508 Sorted by residual: angle pdb=" N ARG B 685 " pdb=" CA ARG B 685 " pdb=" C ARG B 685 " ideal model delta sigma weight residual 113.16 122.65 -9.49 1.24e+00 6.50e-01 5.86e+01 angle pdb=" O1P PEE C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.24 -13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.22 -13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE B 901 " pdb=" P PEE B 901 " pdb=" O2P PEE B 901 " ideal model delta sigma weight residual 119.43 133.13 -13.70 3.00e+00 1.11e-01 2.09e+01 angle pdb=" CA LYS F 555 " pdb=" CB LYS F 555 " pdb=" CG LYS F 555 " ideal model delta sigma weight residual 114.10 122.85 -8.75 2.00e+00 2.50e-01 1.91e+01 ... (remaining 35503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 15328 34.77 - 69.54: 479 69.54 - 104.31: 28 104.31 - 139.08: 2 139.08 - 173.86: 5 Dihedral angle restraints: 15842 sinusoidal: 6664 harmonic: 9178 Sorted by residual: dihedral pdb=" CB CYS C 113 " pdb=" SG CYS C 113 " pdb=" SG CYS C 295 " pdb=" CB CYS C 295 " ideal model delta sinusoidal sigma weight residual 93.00 43.52 49.48 1 1.00e+01 1.00e-02 3.36e+01 dihedral pdb=" N PEE C 901 " pdb=" C4 PEE C 901 " pdb=" C5 PEE C 901 " pdb=" O4P PEE C 901 " ideal model delta sinusoidal sigma weight residual 303.03 129.17 173.86 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 PEE C 901 " pdb=" C1 PEE C 901 " pdb=" C2 PEE C 901 " pdb=" O3P PEE C 901 " ideal model delta sinusoidal sigma weight residual -59.96 111.18 -171.14 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 15839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3279 0.056 - 0.112: 646 0.112 - 0.168: 58 0.168 - 0.224: 6 0.224 - 0.280: 7 Chirality restraints: 3996 Sorted by residual: chirality pdb=" CB VAL E 283 " pdb=" CA VAL E 283 " pdb=" CG1 VAL E 283 " pdb=" CG2 VAL E 283 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB ILE B 677 " pdb=" CA ILE B 677 " pdb=" CG1 ILE B 677 " pdb=" CG2 ILE B 677 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C2 PEE F 901 " pdb=" C1 PEE F 901 " pdb=" C3 PEE F 901 " pdb=" O2 PEE F 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.61 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 3993 not shown) Planarity restraints: 4352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 23 " -0.021 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP F 23 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP F 23 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP F 23 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 23 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 23 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 23 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 23 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 795 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO A 796 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 796 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 796 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 168 " -0.017 2.00e-02 2.50e+03 1.67e-02 6.94e+00 pdb=" CG TRP C 168 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 168 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 168 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 168 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 168 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 168 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 168 " 0.001 2.00e-02 2.50e+03 ... (remaining 4349 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2161 2.74 - 3.28: 25874 3.28 - 3.82: 45070 3.82 - 4.36: 53989 4.36 - 4.90: 89810 Nonbonded interactions: 216904 Sorted by model distance: nonbonded pdb=" NE2 GLN A 46 " pdb=" O LYS A 123 " model vdw 2.206 2.520 nonbonded pdb=" OH TYR B 351 " pdb=" OD2 ASP B 380 " model vdw 2.249 2.440 nonbonded pdb=" O ILE F 556 " pdb=" ND2 ASN F 584 " model vdw 2.258 2.520 nonbonded pdb=" OG1 THR E 303 " pdb=" OH TYR E 308 " model vdw 2.269 2.440 nonbonded pdb=" O PRO D 167 " pdb=" OG1 THR D 170 " model vdw 2.272 2.440 ... (remaining 216899 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 175 or resid 231 through 808 or resid 901 or (r \ esid 902 and (name C10 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name O2 or name O4 )) or (resid 903 an \ d (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C16 or name C17 or name O2 or name O4 )))) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 15 through 402 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name O2 or name O4 ) \ ))) selection = (chain 'D' and (resid 15 through 175 or resid 235 through 402 or resid 902)) selection = (chain 'E' and (resid 15 through 175 or resid 235 through 402 or resid 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 16.360 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 69.040 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.140 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 26274 Z= 0.286 Angle : 0.753 13.805 35508 Z= 0.412 Chirality : 0.044 0.280 3996 Planarity : 0.005 0.072 4352 Dihedral : 16.495 173.856 9821 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.28 % Allowed : 18.72 % Favored : 81.00 % 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: -0.68 (0.15), residues: 3036 helix: 0.29 (0.12), residues: 1636 sheet: -1.73 (0.30), residues: 289 loop : -1.05 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP F 23 HIS 0.021 0.001 HIS D 155 PHE 0.034 0.002 PHE C 142 TYR 0.030 0.002 TYR E 281 ARG 0.009 0.001 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 533 time to evaluate : 3.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7284 (tp30) cc_final: 0.7041 (tp30) REVERT: A 233 ASP cc_start: 0.7744 (t0) cc_final: 0.7068 (t0) REVERT: A 343 MET cc_start: 0.8756 (ttm) cc_final: 0.8215 (ttm) REVERT: A 414 ASP cc_start: 0.9059 (m-30) cc_final: 0.8810 (t0) REVERT: A 478 HIS cc_start: 0.7250 (m170) cc_final: 0.6807 (m-70) REVERT: A 533 ARG cc_start: 0.6007 (ttt180) cc_final: 0.5123 (ptm160) REVERT: A 596 LEU cc_start: 0.6763 (tp) cc_final: 0.6312 (mt) REVERT: A 646 LEU cc_start: 0.9164 (mt) cc_final: 0.8907 (mm) REVERT: A 667 LEU cc_start: 0.8389 (tp) cc_final: 0.8188 (tt) REVERT: B 66 ASN cc_start: 0.5083 (t0) cc_final: 0.4880 (t0) REVERT: B 590 MET cc_start: 0.0815 (tpt) cc_final: 0.0520 (mmt) REVERT: B 687 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5694 (mt) REVERT: C 33 ILE cc_start: 0.8710 (tp) cc_final: 0.8473 (tt) REVERT: C 35 MET cc_start: 0.8212 (mtt) cc_final: 0.7978 (mtm) REVERT: C 59 TRP cc_start: 0.7967 (m100) cc_final: 0.7687 (m100) REVERT: C 286 VAL cc_start: 0.8530 (p) cc_final: 0.8295 (t) REVERT: C 337 MET cc_start: 0.6594 (tmm) cc_final: 0.6297 (tmm) REVERT: C 359 GLU cc_start: 0.5319 (tm-30) cc_final: 0.4938 (mt-10) REVERT: C 375 MET cc_start: 0.6787 (mtm) cc_final: 0.6559 (mtm) REVERT: C 385 LEU cc_start: 0.8123 (tp) cc_final: 0.7819 (tt) REVERT: D 46 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7131 (tt0) REVERT: D 127 TYR cc_start: 0.8621 (m-80) cc_final: 0.8380 (m-80) REVERT: E 265 MET cc_start: 0.7406 (ttp) cc_final: 0.7129 (tmm) REVERT: E 354 GLU cc_start: 0.7199 (pt0) cc_final: 0.6775 (mm-30) REVERT: F 96 MET cc_start: 0.7488 (mmm) cc_final: 0.7075 (mtt) REVERT: F 147 LYS cc_start: 0.4716 (mmmt) cc_final: 0.4481 (ptmt) REVERT: F 166 PHE cc_start: 0.6826 (t80) cc_final: 0.6620 (t80) REVERT: F 323 TYR cc_start: 0.8313 (t80) cc_final: 0.7796 (t80) outliers start: 8 outliers final: 2 residues processed: 540 average time/residue: 0.4452 time to fit residues: 354.2243 Evaluate side-chains 311 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 308 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain F residue 366 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 127 optimal weight: 0.1980 chunk 78 optimal weight: 0.5980 chunk 155 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 238 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 276 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 239 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS D 400 ASN E 141 ASN E 155 HIS ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN ** E 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 ASN F 635 HIS ** F 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26274 Z= 0.224 Angle : 0.583 14.823 35508 Z= 0.293 Chirality : 0.040 0.172 3996 Planarity : 0.004 0.055 4352 Dihedral : 8.819 154.854 3538 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.73 % Allowed : 20.01 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3036 helix: 0.66 (0.13), residues: 1644 sheet: -1.83 (0.30), residues: 295 loop : -0.87 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 168 HIS 0.012 0.001 HIS A 499 PHE 0.025 0.002 PHE F 666 TYR 0.017 0.001 TYR A 668 ARG 0.007 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 340 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 THR cc_start: 0.7777 (m) cc_final: 0.7352 (t) REVERT: A 434 MET cc_start: 0.8470 (mmm) cc_final: 0.7945 (mmm) REVERT: A 440 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7198 (m-30) REVERT: A 468 LEU cc_start: 0.8375 (mt) cc_final: 0.8115 (mt) REVERT: A 478 HIS cc_start: 0.7302 (m170) cc_final: 0.6999 (m-70) REVERT: A 515 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6828 (mm) REVERT: A 533 ARG cc_start: 0.5905 (ttt180) cc_final: 0.5157 (ptm160) REVERT: A 646 LEU cc_start: 0.9122 (mt) cc_final: 0.8837 (mm) REVERT: B 590 MET cc_start: 0.1085 (tpt) cc_final: 0.0799 (mmt) REVERT: C 35 MET cc_start: 0.8151 (mtt) cc_final: 0.7947 (mtt) REVERT: C 59 TRP cc_start: 0.7960 (m100) cc_final: 0.7715 (m100) REVERT: C 262 ARG cc_start: 0.7151 (mtm110) cc_final: 0.6756 (mtm180) REVERT: C 266 ARG cc_start: 0.6747 (mtt180) cc_final: 0.5934 (mtm-85) REVERT: C 375 MET cc_start: 0.6705 (mtm) cc_final: 0.6463 (mtm) REVERT: D 143 TRP cc_start: 0.7203 (OUTLIER) cc_final: 0.6902 (t60) REVERT: D 250 PHE cc_start: 0.6534 (t80) cc_final: 0.6091 (t80) REVERT: D 375 MET cc_start: 0.7355 (mtm) cc_final: 0.6823 (mtm) REVERT: E 354 GLU cc_start: 0.7062 (pt0) cc_final: 0.6662 (pm20) REVERT: F 140 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7565 (mt) REVERT: F 143 ASN cc_start: 0.5837 (OUTLIER) cc_final: 0.5138 (p0) REVERT: F 147 LYS cc_start: 0.4862 (mmmt) cc_final: 0.4466 (ptmt) REVERT: F 242 PHE cc_start: 0.6395 (OUTLIER) cc_final: 0.6153 (t80) REVERT: F 279 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.8082 (p90) REVERT: F 800 MET cc_start: 0.2725 (mmt) cc_final: 0.2519 (mmt) outliers start: 78 outliers final: 36 residues processed: 398 average time/residue: 0.3931 time to fit residues: 243.6747 Evaluate side-chains 328 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 285 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 694 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 378 ASP Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 679 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 229 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 276 optimal weight: 0.3980 chunk 298 optimal weight: 30.0000 chunk 246 optimal weight: 9.9990 chunk 274 optimal weight: 20.0000 chunk 94 optimal weight: 0.5980 chunk 221 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 GLN A 740 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN D 377 HIS ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 515 ASN F 683 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26274 Z= 0.206 Angle : 0.571 17.612 35508 Z= 0.285 Chirality : 0.040 0.317 3996 Planarity : 0.004 0.081 4352 Dihedral : 7.721 159.598 3534 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.97 % Allowed : 20.47 % Favored : 76.56 % 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: -0.12 (0.16), residues: 3036 helix: 0.75 (0.13), residues: 1645 sheet: -1.84 (0.29), residues: 313 loop : -0.65 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 411 HIS 0.006 0.001 HIS E 253 PHE 0.026 0.001 PHE E 324 TYR 0.026 0.001 TYR A 689 ARG 0.008 0.000 ARG D 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 296 time to evaluate : 3.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 THR cc_start: 0.7757 (m) cc_final: 0.7390 (t) REVERT: A 434 MET cc_start: 0.8509 (mmm) cc_final: 0.8221 (mmm) REVERT: A 478 HIS cc_start: 0.7375 (m170) cc_final: 0.7067 (m-70) REVERT: A 512 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8046 (pt) REVERT: A 515 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6982 (mm) REVERT: A 522 HIS cc_start: 0.7498 (m90) cc_final: 0.7151 (m90) REVERT: A 526 ASN cc_start: 0.6534 (t0) cc_final: 0.5392 (m-40) REVERT: A 533 ARG cc_start: 0.5814 (ttt180) cc_final: 0.4945 (ptm160) REVERT: A 646 LEU cc_start: 0.9017 (mt) cc_final: 0.8709 (mm) REVERT: B 641 LEU cc_start: 0.3209 (OUTLIER) cc_final: 0.2884 (pp) REVERT: C 59 TRP cc_start: 0.8040 (m100) cc_final: 0.7726 (m100) REVERT: C 262 ARG cc_start: 0.7174 (mtm110) cc_final: 0.6949 (mtm110) REVERT: C 266 ARG cc_start: 0.6757 (mtt180) cc_final: 0.6008 (mtm-85) REVERT: C 375 MET cc_start: 0.6765 (mtm) cc_final: 0.6468 (mtm) REVERT: D 143 TRP cc_start: 0.7323 (OUTLIER) cc_final: 0.6995 (t60) REVERT: D 250 PHE cc_start: 0.6511 (t80) cc_final: 0.6122 (t80) REVERT: E 354 GLU cc_start: 0.7073 (pt0) cc_final: 0.6643 (pm20) REVERT: E 375 MET cc_start: 0.7231 (mtm) cc_final: 0.6987 (mtt) REVERT: F 140 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7583 (mt) REVERT: F 143 ASN cc_start: 0.5936 (OUTLIER) cc_final: 0.5347 (p0) REVERT: F 147 LYS cc_start: 0.4917 (mmmt) cc_final: 0.4498 (ptmt) REVERT: F 170 TRP cc_start: 0.5367 (t-100) cc_final: 0.5137 (t-100) REVERT: F 242 PHE cc_start: 0.6251 (OUTLIER) cc_final: 0.5864 (t80) REVERT: F 279 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.8135 (p90) outliers start: 85 outliers final: 44 residues processed: 354 average time/residue: 0.3807 time to fit residues: 213.3088 Evaluate side-chains 316 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 264 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 729 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 475 TRP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 378 ASP Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 657 LYS Chi-restraints excluded: chain F residue 679 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 277 optimal weight: 0.9990 chunk 293 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 263 optimal weight: 0.8980 chunk 79 optimal weight: 0.0370 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 755 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 HIS ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 400 ASN ** F 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26274 Z= 0.197 Angle : 0.546 12.603 35508 Z= 0.276 Chirality : 0.040 0.270 3996 Planarity : 0.004 0.035 4352 Dihedral : 7.199 162.690 3533 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.11 % Allowed : 20.85 % Favored : 76.03 % 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: -0.06 (0.16), residues: 3036 helix: 0.80 (0.13), residues: 1652 sheet: -1.72 (0.30), residues: 311 loop : -0.69 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 411 HIS 0.004 0.001 HIS A 104 PHE 0.027 0.001 PHE E 324 TYR 0.018 0.001 TYR F 646 ARG 0.007 0.000 ARG B 545 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 294 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 THR cc_start: 0.7732 (m) cc_final: 0.7370 (t) REVERT: A 434 MET cc_start: 0.8617 (mmm) cc_final: 0.8195 (mmm) REVERT: A 448 LEU cc_start: 0.7697 (mt) cc_final: 0.7239 (mt) REVERT: A 478 HIS cc_start: 0.7345 (m170) cc_final: 0.7039 (m-70) REVERT: A 512 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8026 (pt) REVERT: A 515 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7054 (mm) REVERT: A 526 ASN cc_start: 0.6433 (t0) cc_final: 0.5362 (m-40) REVERT: A 533 ARG cc_start: 0.5755 (ttt180) cc_final: 0.4822 (ptm160) REVERT: A 568 HIS cc_start: 0.5752 (OUTLIER) cc_final: 0.5523 (p-80) REVERT: A 581 LEU cc_start: 0.4682 (OUTLIER) cc_final: 0.4426 (mm) REVERT: A 646 LEU cc_start: 0.8954 (mt) cc_final: 0.8672 (mm) REVERT: B 456 ILE cc_start: 0.6194 (mm) cc_final: 0.5974 (mm) REVERT: B 590 MET cc_start: 0.3409 (mmt) cc_final: 0.2981 (mmt) REVERT: B 641 LEU cc_start: 0.3401 (OUTLIER) cc_final: 0.3114 (pp) REVERT: B 779 LEU cc_start: 0.2603 (OUTLIER) cc_final: 0.1813 (tp) REVERT: C 59 TRP cc_start: 0.8034 (m100) cc_final: 0.7761 (m100) REVERT: C 262 ARG cc_start: 0.7189 (mtm110) cc_final: 0.6954 (mtm110) REVERT: C 263 LEU cc_start: 0.7068 (mt) cc_final: 0.6841 (mt) REVERT: C 266 ARG cc_start: 0.6779 (mtt180) cc_final: 0.6010 (mtm-85) REVERT: D 143 TRP cc_start: 0.7436 (OUTLIER) cc_final: 0.7001 (t60) REVERT: D 250 PHE cc_start: 0.6370 (t80) cc_final: 0.6054 (t80) REVERT: D 375 MET cc_start: 0.7191 (mtm) cc_final: 0.6620 (mtm) REVERT: E 24 TRP cc_start: 0.7221 (p90) cc_final: 0.6756 (p90) REVERT: E 245 GLU cc_start: 0.7830 (tp30) cc_final: 0.7361 (tp30) REVERT: E 354 GLU cc_start: 0.6987 (pt0) cc_final: 0.6572 (pm20) REVERT: F 140 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7647 (mt) REVERT: F 143 ASN cc_start: 0.5918 (OUTLIER) cc_final: 0.5656 (p0) REVERT: F 242 PHE cc_start: 0.6444 (OUTLIER) cc_final: 0.5963 (t80) REVERT: F 458 MET cc_start: 0.4824 (tpt) cc_final: 0.4079 (tpt) REVERT: F 480 LYS cc_start: 0.6591 (pttm) cc_final: 0.6208 (pttm) outliers start: 89 outliers final: 44 residues processed: 352 average time/residue: 0.3745 time to fit residues: 209.8872 Evaluate side-chains 324 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 270 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 475 TRP Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 378 ASP Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 616 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 150 optimal weight: 0.0980 chunk 263 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26274 Z= 0.184 Angle : 0.538 11.837 35508 Z= 0.270 Chirality : 0.040 0.294 3996 Planarity : 0.004 0.052 4352 Dihedral : 6.895 164.085 3533 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.90 % Allowed : 21.17 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.16), residues: 3036 helix: 0.84 (0.13), residues: 1660 sheet: -1.66 (0.30), residues: 311 loop : -0.66 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 411 HIS 0.004 0.001 HIS A 104 PHE 0.027 0.001 PHE E 324 TYR 0.024 0.001 TYR F 323 ARG 0.006 0.000 ARG B 545 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 286 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 THR cc_start: 0.7658 (m) cc_final: 0.7382 (t) REVERT: A 434 MET cc_start: 0.8480 (mmm) cc_final: 0.8269 (mmm) REVERT: A 448 LEU cc_start: 0.7691 (mt) cc_final: 0.7096 (mt) REVERT: A 478 HIS cc_start: 0.7313 (m170) cc_final: 0.7089 (m-70) REVERT: A 512 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8074 (pt) REVERT: A 515 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7082 (mm) REVERT: A 526 ASN cc_start: 0.6308 (t0) cc_final: 0.5210 (m-40) REVERT: A 533 ARG cc_start: 0.5731 (ttt180) cc_final: 0.4811 (ptm160) REVERT: A 581 LEU cc_start: 0.4628 (OUTLIER) cc_final: 0.4376 (mm) REVERT: A 646 LEU cc_start: 0.8949 (mt) cc_final: 0.8691 (mm) REVERT: B 590 MET cc_start: 0.3481 (mmt) cc_final: 0.3068 (mmt) REVERT: B 641 LEU cc_start: 0.3313 (OUTLIER) cc_final: 0.3097 (pp) REVERT: B 779 LEU cc_start: 0.2474 (OUTLIER) cc_final: 0.1758 (tp) REVERT: C 59 TRP cc_start: 0.8029 (m100) cc_final: 0.7768 (m100) REVERT: C 262 ARG cc_start: 0.7198 (mtm110) cc_final: 0.6935 (mtm110) REVERT: C 266 ARG cc_start: 0.6805 (mtt180) cc_final: 0.6036 (mtm-85) REVERT: D 143 TRP cc_start: 0.7419 (OUTLIER) cc_final: 0.6994 (t60) REVERT: D 250 PHE cc_start: 0.6406 (t80) cc_final: 0.6163 (t80) REVERT: E 24 TRP cc_start: 0.7228 (p90) cc_final: 0.6756 (p90) REVERT: E 354 GLU cc_start: 0.6991 (pt0) cc_final: 0.6579 (pm20) REVERT: E 400 ASN cc_start: 0.7615 (p0) cc_final: 0.7279 (m-40) REVERT: F 140 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7745 (mt) REVERT: F 143 ASN cc_start: 0.5883 (OUTLIER) cc_final: 0.5648 (p0) REVERT: F 170 TRP cc_start: 0.5512 (t-100) cc_final: 0.5265 (t-100) REVERT: F 242 PHE cc_start: 0.6457 (OUTLIER) cc_final: 0.5983 (t80) REVERT: F 353 TYR cc_start: 0.6719 (p90) cc_final: 0.6513 (p90) REVERT: F 480 LYS cc_start: 0.6533 (pttm) cc_final: 0.6178 (pttt) outliers start: 83 outliers final: 50 residues processed: 346 average time/residue: 0.3730 time to fit residues: 204.8511 Evaluate side-chains 329 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 270 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 734 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 475 TRP Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 573 HIS Chi-restraints excluded: chain F residue 616 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 172 optimal weight: 0.0670 chunk 72 optimal weight: 1.9990 chunk 294 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN B 709 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26274 Z= 0.172 Angle : 0.523 10.325 35508 Z= 0.264 Chirality : 0.040 0.276 3996 Planarity : 0.004 0.053 4352 Dihedral : 6.637 164.697 3533 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.76 % Allowed : 21.41 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 3036 helix: 0.90 (0.13), residues: 1657 sheet: -1.64 (0.30), residues: 306 loop : -0.57 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP B 411 HIS 0.005 0.001 HIS F 475 PHE 0.028 0.001 PHE A 443 TYR 0.021 0.001 TYR F 279 ARG 0.008 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 294 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 THR cc_start: 0.7614 (m) cc_final: 0.7349 (t) REVERT: A 448 LEU cc_start: 0.7728 (mt) cc_final: 0.7225 (mt) REVERT: A 478 HIS cc_start: 0.7373 (m170) cc_final: 0.7022 (m-70) REVERT: A 506 LYS cc_start: 0.7523 (tptp) cc_final: 0.6905 (pttp) REVERT: A 512 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8023 (pt) REVERT: A 526 ASN cc_start: 0.6261 (t0) cc_final: 0.5274 (p0) REVERT: A 533 ARG cc_start: 0.5855 (ttt180) cc_final: 0.4849 (ptm160) REVERT: A 581 LEU cc_start: 0.4639 (OUTLIER) cc_final: 0.4379 (mm) REVERT: A 646 LEU cc_start: 0.8943 (mt) cc_final: 0.8677 (mm) REVERT: B 456 ILE cc_start: 0.5927 (mm) cc_final: 0.5449 (mm) REVERT: B 667 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6425 (tp) REVERT: B 779 LEU cc_start: 0.2282 (OUTLIER) cc_final: 0.1797 (tp) REVERT: C 59 TRP cc_start: 0.8032 (m100) cc_final: 0.7767 (m100) REVERT: C 263 LEU cc_start: 0.6878 (mt) cc_final: 0.6650 (mt) REVERT: C 266 ARG cc_start: 0.6810 (mtt180) cc_final: 0.6069 (mtm-85) REVERT: D 143 TRP cc_start: 0.7349 (OUTLIER) cc_final: 0.6830 (t60) REVERT: D 250 PHE cc_start: 0.6337 (t80) cc_final: 0.6116 (t80) REVERT: D 375 MET cc_start: 0.7171 (mtm) cc_final: 0.6745 (mtm) REVERT: E 354 GLU cc_start: 0.6989 (pt0) cc_final: 0.6578 (pm20) REVERT: F 140 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7782 (mt) REVERT: F 242 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.5979 (t80) REVERT: F 800 MET cc_start: 0.1594 (mmt) cc_final: 0.0921 (mmm) outliers start: 79 outliers final: 53 residues processed: 345 average time/residue: 0.3693 time to fit residues: 203.3936 Evaluate side-chains 325 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 265 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 475 TRP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 573 HIS Chi-restraints excluded: chain F residue 616 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 247 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 chunk 293 optimal weight: 0.0370 chunk 183 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 606 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26274 Z= 0.180 Angle : 0.553 15.616 35508 Z= 0.275 Chirality : 0.040 0.343 3996 Planarity : 0.004 0.054 4352 Dihedral : 6.502 165.490 3533 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.87 % Allowed : 21.55 % Favored : 75.58 % 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: 0.16 (0.16), residues: 3036 helix: 0.96 (0.13), residues: 1651 sheet: -1.58 (0.30), residues: 315 loop : -0.55 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 411 HIS 0.005 0.001 HIS A 431 PHE 0.030 0.001 PHE A 443 TYR 0.022 0.001 TYR F 279 ARG 0.017 0.000 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 280 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9121 (tp) cc_final: 0.8842 (mt) REVERT: A 415 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7886 (pttt) REVERT: A 434 MET cc_start: 0.8292 (mmm) cc_final: 0.7857 (mmm) REVERT: A 443 PHE cc_start: 0.4068 (t80) cc_final: 0.3808 (t80) REVERT: A 448 LEU cc_start: 0.7772 (mt) cc_final: 0.7270 (mt) REVERT: A 478 HIS cc_start: 0.7432 (m170) cc_final: 0.7183 (m-70) REVERT: A 506 LYS cc_start: 0.7731 (tptp) cc_final: 0.7326 (pptt) REVERT: A 511 TRP cc_start: 0.7226 (m100) cc_final: 0.6977 (m-90) REVERT: A 526 ASN cc_start: 0.6272 (t0) cc_final: 0.5276 (p0) REVERT: A 533 ARG cc_start: 0.5787 (ttt180) cc_final: 0.4738 (ptm160) REVERT: A 544 LYS cc_start: 0.6084 (OUTLIER) cc_final: 0.5077 (ptpp) REVERT: A 581 LEU cc_start: 0.4652 (OUTLIER) cc_final: 0.4401 (mm) REVERT: A 646 LEU cc_start: 0.8995 (mt) cc_final: 0.8753 (mm) REVERT: B 456 ILE cc_start: 0.5976 (mm) cc_final: 0.5430 (tt) REVERT: B 667 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6444 (tp) REVERT: B 779 LEU cc_start: 0.1923 (OUTLIER) cc_final: 0.1459 (tp) REVERT: C 59 TRP cc_start: 0.8036 (m100) cc_final: 0.7752 (m100) REVERT: C 266 ARG cc_start: 0.6821 (mtt180) cc_final: 0.6157 (mtm-85) REVERT: D 143 TRP cc_start: 0.7396 (OUTLIER) cc_final: 0.6865 (t60) REVERT: D 167 PRO cc_start: 0.7053 (Cg_exo) cc_final: 0.6770 (Cg_endo) REVERT: D 250 PHE cc_start: 0.6331 (t80) cc_final: 0.6117 (t80) REVERT: D 375 MET cc_start: 0.7180 (mtm) cc_final: 0.6684 (mtm) REVERT: E 354 GLU cc_start: 0.6988 (pt0) cc_final: 0.6579 (pm20) REVERT: F 140 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7801 (mt) REVERT: F 143 ASN cc_start: 0.5799 (OUTLIER) cc_final: 0.5598 (p0) REVERT: F 242 PHE cc_start: 0.6609 (OUTLIER) cc_final: 0.6225 (t80) REVERT: F 323 TYR cc_start: 0.8285 (t80) cc_final: 0.7823 (t80) outliers start: 82 outliers final: 59 residues processed: 338 average time/residue: 0.3532 time to fit residues: 192.9137 Evaluate side-chains 335 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 268 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 734 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 475 TRP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 143 TRP Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 456 ASN Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 573 HIS Chi-restraints excluded: chain F residue 766 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 230 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS E 155 HIS E 381 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 26274 Z= 0.333 Angle : 0.612 13.947 35508 Z= 0.309 Chirality : 0.043 0.265 3996 Planarity : 0.004 0.045 4352 Dihedral : 6.900 177.637 3533 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.18 % Allowed : 21.52 % Favored : 75.30 % 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: -0.19 (0.15), residues: 3036 helix: 0.65 (0.13), residues: 1674 sheet: -1.64 (0.30), residues: 316 loop : -0.71 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 411 HIS 0.005 0.001 HIS D 312 PHE 0.035 0.002 PHE E 324 TYR 0.023 0.002 TYR F 279 ARG 0.007 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 282 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8327 (mmm) cc_final: 0.8031 (mmm) REVERT: A 448 LEU cc_start: 0.7831 (mt) cc_final: 0.7363 (mt) REVERT: A 478 HIS cc_start: 0.7480 (m170) cc_final: 0.7223 (m-70) REVERT: A 488 LEU cc_start: 0.8484 (tp) cc_final: 0.8256 (tp) REVERT: A 506 LYS cc_start: 0.7874 (tptp) cc_final: 0.7436 (pptt) REVERT: A 511 TRP cc_start: 0.7306 (m100) cc_final: 0.6954 (m-90) REVERT: A 533 ARG cc_start: 0.5875 (ttt180) cc_final: 0.4729 (ptm160) REVERT: A 544 LYS cc_start: 0.6075 (OUTLIER) cc_final: 0.5073 (ptpp) REVERT: A 581 LEU cc_start: 0.4761 (OUTLIER) cc_final: 0.4522 (mm) REVERT: A 613 LEU cc_start: 0.1585 (OUTLIER) cc_final: 0.1319 (mp) REVERT: A 646 LEU cc_start: 0.8954 (mt) cc_final: 0.8736 (mm) REVERT: B 456 ILE cc_start: 0.5673 (mm) cc_final: 0.5099 (tt) REVERT: B 779 LEU cc_start: 0.1701 (OUTLIER) cc_final: 0.1070 (tp) REVERT: C 59 TRP cc_start: 0.8024 (m100) cc_final: 0.7805 (m100) REVERT: C 266 ARG cc_start: 0.6988 (mtt180) cc_final: 0.4926 (ttp80) REVERT: D 143 TRP cc_start: 0.7591 (OUTLIER) cc_final: 0.7161 (t60) REVERT: D 353 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.5773 (m-80) REVERT: E 59 TRP cc_start: 0.6610 (m-90) cc_final: 0.6328 (m-90) REVERT: F 140 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7840 (mt) REVERT: F 170 TRP cc_start: 0.5583 (t-100) cc_final: 0.5346 (t-100) REVERT: F 242 PHE cc_start: 0.6851 (OUTLIER) cc_final: 0.6212 (t80) outliers start: 91 outliers final: 63 residues processed: 346 average time/residue: 0.3714 time to fit residues: 206.7828 Evaluate side-chains 331 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 260 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 734 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 475 TRP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 143 TRP Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 573 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 679 LEU Chi-restraints excluded: chain F residue 766 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 7.9990 chunk 280 optimal weight: 30.0000 chunk 256 optimal weight: 0.7980 chunk 273 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 272 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 ASN D 404 GLN E 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 26274 Z= 0.384 Angle : 0.636 15.027 35508 Z= 0.321 Chirality : 0.043 0.244 3996 Planarity : 0.004 0.049 4352 Dihedral : 6.931 173.848 3533 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.69 % Allowed : 22.29 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3036 helix: 0.54 (0.13), residues: 1666 sheet: -1.54 (0.30), residues: 315 loop : -0.80 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP B 411 HIS 0.006 0.001 HIS D 312 PHE 0.034 0.002 PHE E 324 TYR 0.039 0.002 TYR F 323 ARG 0.009 0.001 ARG D 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 270 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: A 385 LEU cc_start: 0.8488 (tp) cc_final: 0.8020 (tp) REVERT: A 415 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7938 (pttt) REVERT: A 434 MET cc_start: 0.8340 (mmm) cc_final: 0.8070 (mmm) REVERT: A 448 LEU cc_start: 0.7874 (mt) cc_final: 0.7484 (mt) REVERT: A 478 HIS cc_start: 0.7387 (m170) cc_final: 0.7128 (m-70) REVERT: A 488 LEU cc_start: 0.8440 (tp) cc_final: 0.8202 (tp) REVERT: A 506 LYS cc_start: 0.7913 (tptp) cc_final: 0.7445 (pptt) REVERT: A 511 TRP cc_start: 0.7382 (m100) cc_final: 0.7058 (m-90) REVERT: A 533 ARG cc_start: 0.5590 (ttt180) cc_final: 0.4368 (ptm160) REVERT: A 544 LYS cc_start: 0.6078 (OUTLIER) cc_final: 0.5050 (ptpp) REVERT: A 581 LEU cc_start: 0.4553 (OUTLIER) cc_final: 0.4321 (mm) REVERT: A 667 LEU cc_start: 0.8220 (pt) cc_final: 0.7769 (tp) REVERT: A 767 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6303 (mm-30) REVERT: B 456 ILE cc_start: 0.5777 (mm) cc_final: 0.5236 (mm) REVERT: B 498 LEU cc_start: 0.6324 (mm) cc_final: 0.6001 (mt) REVERT: C 59 TRP cc_start: 0.8005 (m100) cc_final: 0.7757 (m100) REVERT: C 266 ARG cc_start: 0.6999 (mtt180) cc_final: 0.4947 (ttp80) REVERT: D 143 TRP cc_start: 0.7551 (OUTLIER) cc_final: 0.7193 (t60) REVERT: D 405 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7515 (tp) REVERT: E 59 TRP cc_start: 0.6753 (m-90) cc_final: 0.6485 (m-90) REVERT: F 140 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7925 (mt) REVERT: F 242 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.6185 (t80) REVERT: F 373 MET cc_start: 0.7127 (mmm) cc_final: 0.6711 (mmt) outliers start: 77 outliers final: 61 residues processed: 327 average time/residue: 0.3380 time to fit residues: 179.1600 Evaluate side-chains 324 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 256 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 734 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 404 GLN Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 143 TRP Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 573 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 679 LEU Chi-restraints excluded: chain F residue 766 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 0.6980 chunk 288 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 302 optimal weight: 0.5980 chunk 278 optimal weight: 9.9990 chunk 241 optimal weight: 0.9990 chunk 25 optimal weight: 0.0030 chunk 186 optimal weight: 9.9990 chunk 147 optimal weight: 0.0270 overall best weight: 0.4248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 ASN D 377 HIS E 155 HIS ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26274 Z= 0.161 Angle : 0.591 15.417 35508 Z= 0.290 Chirality : 0.041 0.244 3996 Planarity : 0.004 0.043 4352 Dihedral : 6.519 169.724 3533 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.96 % Allowed : 23.20 % Favored : 74.84 % 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: -0.09 (0.16), residues: 3036 helix: 0.71 (0.13), residues: 1666 sheet: -1.44 (0.30), residues: 314 loop : -0.69 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP B 411 HIS 0.005 0.001 HIS A 431 PHE 0.028 0.001 PHE E 324 TYR 0.035 0.001 TYR F 323 ARG 0.009 0.000 ARG A 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 281 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9155 (tp) cc_final: 0.8925 (mt) REVERT: A 385 LEU cc_start: 0.8458 (tp) cc_final: 0.8019 (tp) REVERT: A 415 LYS cc_start: 0.8147 (mtmt) cc_final: 0.7918 (pttt) REVERT: A 434 MET cc_start: 0.8270 (mmm) cc_final: 0.8016 (mmm) REVERT: A 438 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8026 (mt) REVERT: A 448 LEU cc_start: 0.7828 (mt) cc_final: 0.7401 (mt) REVERT: A 478 HIS cc_start: 0.7348 (m170) cc_final: 0.7094 (m-70) REVERT: A 488 LEU cc_start: 0.8453 (tp) cc_final: 0.8224 (tp) REVERT: A 506 LYS cc_start: 0.8021 (tptp) cc_final: 0.7544 (pptt) REVERT: A 511 TRP cc_start: 0.7414 (m100) cc_final: 0.7077 (m-90) REVERT: A 533 ARG cc_start: 0.5482 (ttt180) cc_final: 0.4297 (ptm160) REVERT: A 544 LYS cc_start: 0.5977 (OUTLIER) cc_final: 0.5250 (mmtt) REVERT: A 581 LEU cc_start: 0.4512 (OUTLIER) cc_final: 0.4295 (mm) REVERT: A 667 LEU cc_start: 0.8141 (pt) cc_final: 0.7720 (tp) REVERT: A 767 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6284 (mm-30) REVERT: B 456 ILE cc_start: 0.5471 (mm) cc_final: 0.5001 (tt) REVERT: B 498 LEU cc_start: 0.6247 (mm) cc_final: 0.5951 (mt) REVERT: B 590 MET cc_start: 0.2435 (mmm) cc_final: 0.1794 (mmm) REVERT: C 266 ARG cc_start: 0.6873 (mtt180) cc_final: 0.4862 (ttp80) REVERT: D 143 TRP cc_start: 0.7445 (OUTLIER) cc_final: 0.6904 (t60) REVERT: D 325 TYR cc_start: 0.8220 (t80) cc_final: 0.7705 (t80) REVERT: E 59 TRP cc_start: 0.6792 (m-90) cc_final: 0.6479 (m-90) REVERT: F 242 PHE cc_start: 0.6793 (OUTLIER) cc_final: 0.6256 (t80) REVERT: F 323 TYR cc_start: 0.8315 (t80) cc_final: 0.7929 (t80) REVERT: F 480 LYS cc_start: 0.6192 (pttm) cc_final: 0.5991 (pttt) REVERT: F 800 MET cc_start: 0.1871 (mmt) cc_final: 0.0493 (mmp) outliers start: 56 outliers final: 42 residues processed: 325 average time/residue: 0.3593 time to fit residues: 188.4374 Evaluate side-chains 314 residues out of total 2858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 267 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 734 ARG Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 143 TRP Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 573 HIS Chi-restraints excluded: chain F residue 627 ILE Chi-restraints excluded: chain F residue 766 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS E 155 HIS ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.196165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.129749 restraints weight = 40706.511| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 4.40 r_work: 0.3424 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26274 Z= 0.206 Angle : 0.588 15.286 35508 Z= 0.291 Chirality : 0.041 0.245 3996 Planarity : 0.004 0.041 4352 Dihedral : 6.390 171.261 3533 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.89 % Allowed : 23.44 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 3036 helix: 0.71 (0.13), residues: 1669 sheet: -1.45 (0.30), residues: 319 loop : -0.68 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP F 170 HIS 0.004 0.001 HIS E 253 PHE 0.030 0.001 PHE E 324 TYR 0.033 0.001 TYR F 323 ARG 0.004 0.000 ARG A 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6508.12 seconds wall clock time: 118 minutes 40.22 seconds (7120.22 seconds total)