Starting phenix.real_space_refine on Sun Mar 17 04:14:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc7_16557/03_2024/8cc7_16557_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc7_16557/03_2024/8cc7_16557.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc7_16557/03_2024/8cc7_16557_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc7_16557/03_2024/8cc7_16557_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc7_16557/03_2024/8cc7_16557_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc7_16557/03_2024/8cc7_16557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc7_16557/03_2024/8cc7_16557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc7_16557/03_2024/8cc7_16557_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cc7_16557/03_2024/8cc7_16557_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.052 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 S 50 5.16 5 Cl 5 4.86 5 C 10960 2.51 5 N 2690 2.21 5 O 2945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 17": "OD1" <-> "OD2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "D TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 421": "OE1" <-> "OE2" Residue "E PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 250": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16650 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3231 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "B" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3231 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "C" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3231 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "D" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3231 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "E" Number of atoms: 3231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3231 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 20, 'TRANS': 369} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'NAG': 1, 'U9Q': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'NAG': 1, 'U9Q': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'NAG': 1, 'U9Q': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'NAG': 1, 'U9Q': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'NAG': 1, 'U9Q': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.67, per 1000 atoms: 0.52 Number of scatterers: 16650 At special positions: 0 Unit cell: (95.035, 96.18, 169.46, 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) Cl 5 17.00 S 50 16.00 O 2945 8.00 N 2690 7.00 C 10960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG B 501 " - " ASN B 82 " " NAG C 501 " - " ASN C 82 " " NAG D 501 " - " ASN D 82 " " NAG E 502 " - " ASN E 82 " " NAG F 1 " - " ASN A 164 " " NAG G 1 " - " ASN A 148 " " NAG H 1 " - " ASN B 164 " " NAG I 1 " - " ASN B 148 " " NAG J 1 " - " ASN C 164 " " NAG K 1 " - " ASN C 148 " " NAG L 1 " - " ASN D 164 " " NAG M 1 " - " ASN D 148 " " NAG N 1 " - " ASN E 164 " " NAG O 1 " - " ASN E 148 " Time building additional restraints: 7.10 Conformation dependent library (CDL) restraints added in 2.6 seconds 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3790 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 20 sheets defined 44.4% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 224 through 243 removed outlier: 3.789A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.917A pdb=" N CYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 251 through 271 removed outlier: 3.997A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 308 Processing helix chain 'A' and resid 319 through 332 removed outlier: 3.790A pdb=" N ILE A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 459 removed outlier: 3.740A pdb=" N GLU A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 220 through 243 removed outlier: 3.711A pdb=" N ALA B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU B 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU B 229 " --> pdb=" O SER B 226 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 251 through 271 removed outlier: 3.991A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 308 Processing helix chain 'B' and resid 319 through 332 removed outlier: 3.799A pdb=" N ILE B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 459 removed outlier: 3.728A pdb=" N GLU B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 20 Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 224 through 243 removed outlier: 3.797A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix removed outlier: 3.927A pdb=" N CYS C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'C' and resid 251 through 271 removed outlier: 3.997A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 308 Processing helix chain 'C' and resid 319 through 332 removed outlier: 3.820A pdb=" N ILE C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 459 removed outlier: 3.753A pdb=" N GLU C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 20 Processing helix chain 'D' and resid 77 through 79 No H-bonds generated for 'chain 'D' and resid 77 through 79' Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 224 through 243 removed outlier: 3.803A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix removed outlier: 3.936A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 248 No H-bonds generated for 'chain 'D' and resid 246 through 248' Processing helix chain 'D' and resid 251 through 271 removed outlier: 3.995A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 308 Processing helix chain 'D' and resid 319 through 332 removed outlier: 3.828A pdb=" N ILE D 329 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 459 removed outlier: 3.756A pdb=" N GLU D 405 " --> pdb=" O GLY D 401 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 20 Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 220 through 222 No H-bonds generated for 'chain 'E' and resid 220 through 222' Processing helix chain 'E' and resid 224 through 243 removed outlier: 3.787A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix removed outlier: 3.933A pdb=" N CYS E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 248 No H-bonds generated for 'chain 'E' and resid 246 through 248' Processing helix chain 'E' and resid 251 through 271 removed outlier: 4.002A pdb=" N ASP E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 308 Processing helix chain 'E' and resid 319 through 332 removed outlier: 3.823A pdb=" N ILE E 329 " --> pdb=" O VAL E 325 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 459 removed outlier: 3.743A pdb=" N GLU E 405 " --> pdb=" O GLY E 401 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.157A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 50 through 52 Processing sheet with id= C, first strand: chain 'A' and resid 85 through 89 Processing sheet with id= D, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.217A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.143A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 50 through 52 Processing sheet with id= G, first strand: chain 'B' and resid 85 through 89 Processing sheet with id= H, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.204A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.155A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 50 through 52 Processing sheet with id= K, first strand: chain 'C' and resid 85 through 89 Processing sheet with id= L, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.232A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.165A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 50 through 52 Processing sheet with id= O, first strand: chain 'D' and resid 85 through 89 Processing sheet with id= P, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.226A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 163 through 167 removed outlier: 6.159A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 50 through 52 Processing sheet with id= S, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= T, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.230A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 837 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.65 Time building geometry restraints manager: 7.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5055 1.34 - 1.46: 4085 1.46 - 1.58: 7890 1.58 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 17115 Sorted by residual: bond pdb=" C06 U9Q E 501 " pdb=" S08 U9Q E 501 " ideal model delta sigma weight residual 1.828 1.696 0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" C06 U9Q A 502 " pdb=" S08 U9Q A 502 " ideal model delta sigma weight residual 1.828 1.697 0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" C06 U9Q D 502 " pdb=" S08 U9Q D 502 " ideal model delta sigma weight residual 1.828 1.697 0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C06 U9Q B 502 " pdb=" S08 U9Q B 502 " ideal model delta sigma weight residual 1.828 1.697 0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C06 U9Q C 502 " pdb=" S08 U9Q C 502 " ideal model delta sigma weight residual 1.828 1.697 0.131 2.00e-02 2.50e+03 4.28e+01 ... (remaining 17110 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.50: 544 106.50 - 113.82: 9903 113.82 - 121.13: 8399 121.13 - 128.45: 4354 128.45 - 135.76: 200 Bond angle restraints: 23400 Sorted by residual: angle pdb=" N22 U9Q B 502 " pdb=" C23 U9Q B 502 " pdb=" N24 U9Q B 502 " ideal model delta sigma weight residual 90.14 122.67 -32.53 3.00e+00 1.11e-01 1.18e+02 angle pdb=" N22 U9Q C 502 " pdb=" C23 U9Q C 502 " pdb=" N24 U9Q C 502 " ideal model delta sigma weight residual 90.14 122.57 -32.43 3.00e+00 1.11e-01 1.17e+02 angle pdb=" N22 U9Q D 502 " pdb=" C23 U9Q D 502 " pdb=" N24 U9Q D 502 " ideal model delta sigma weight residual 90.14 122.56 -32.42 3.00e+00 1.11e-01 1.17e+02 angle pdb=" N22 U9Q E 501 " pdb=" C23 U9Q E 501 " pdb=" N24 U9Q E 501 " ideal model delta sigma weight residual 90.14 122.54 -32.40 3.00e+00 1.11e-01 1.17e+02 angle pdb=" N22 U9Q A 502 " pdb=" C23 U9Q A 502 " pdb=" N24 U9Q A 502 " ideal model delta sigma weight residual 90.14 122.53 -32.39 3.00e+00 1.11e-01 1.17e+02 ... (remaining 23395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.49: 9518 23.49 - 46.98: 732 46.98 - 70.46: 50 70.46 - 93.95: 25 93.95 - 117.44: 25 Dihedral angle restraints: 10350 sinusoidal: 4535 harmonic: 5815 Sorted by residual: dihedral pdb=" C14 U9Q E 501 " pdb=" C23 U9Q E 501 " pdb=" N24 U9Q E 501 " pdb=" C25 U9Q E 501 " ideal model delta sinusoidal sigma weight residual 182.63 65.19 117.44 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" C14 U9Q B 502 " pdb=" C23 U9Q B 502 " pdb=" N24 U9Q B 502 " pdb=" C25 U9Q B 502 " ideal model delta sinusoidal sigma weight residual 182.63 65.33 117.30 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" C14 U9Q C 502 " pdb=" C23 U9Q C 502 " pdb=" N24 U9Q C 502 " pdb=" C25 U9Q C 502 " ideal model delta sinusoidal sigma weight residual 182.63 65.44 117.19 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 10347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1645 0.029 - 0.057: 656 0.057 - 0.086: 243 0.086 - 0.114: 165 0.114 - 0.143: 51 Chirality restraints: 2760 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 148 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN E 148 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 148 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 2757 not shown) Planarity restraints: 2835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 456 " 0.009 2.00e-02 2.50e+03 9.16e-03 2.10e+00 pdb=" CG TRP C 456 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP C 456 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP C 456 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 456 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 456 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 456 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 456 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 456 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 456 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 456 " 0.009 2.00e-02 2.50e+03 8.82e-03 1.95e+00 pdb=" CG TRP E 456 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP E 456 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP E 456 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 456 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 456 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 456 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 456 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 456 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 456 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 456 " 0.008 2.00e-02 2.50e+03 8.06e-03 1.62e+00 pdb=" CG TRP B 456 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP B 456 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 456 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 456 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 456 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 456 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 456 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 456 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 456 " 0.000 2.00e-02 2.50e+03 ... (remaining 2832 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2785 2.77 - 3.30: 15818 3.30 - 3.84: 28730 3.84 - 4.37: 31803 4.37 - 4.90: 57457 Nonbonded interactions: 136593 Sorted by model distance: nonbonded pdb=" OE2 GLU E 53 " pdb=" NH2 ARG E 218 " model vdw 2.239 2.520 nonbonded pdb=" OE2 GLU A 53 " pdb=" NH2 ARG A 218 " model vdw 2.243 2.520 nonbonded pdb=" OE2 GLU B 53 " pdb=" NH2 ARG B 218 " model vdw 2.248 2.520 nonbonded pdb=" O HIS A 309 " pdb=" NE2 GLN A 314 " model vdw 2.248 2.520 nonbonded pdb=" O HIS D 309 " pdb=" NE2 GLN D 314 " model vdw 2.249 2.520 ... (remaining 136588 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 8 through 460) selection = (chain 'B' and resid 8 through 460) selection = (chain 'C' and resid 8 through 460) selection = (chain 'D' and resid 8 through 460) selection = (chain 'E' and resid 8 through 460) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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=0.00 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.390 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 44.040 Find NCS groups from input model: 1.150 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:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 0.132 17115 Z= 0.323 Angle : 0.875 32.526 23400 Z= 0.356 Chirality : 0.042 0.143 2760 Planarity : 0.004 0.037 2820 Dihedral : 16.557 117.440 6560 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.55 % Allowed : 19.40 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.20), residues: 1930 helix: 3.34 (0.17), residues: 780 sheet: -0.82 (0.23), residues: 440 loop : 0.57 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 456 HIS 0.002 0.001 HIS C 18 PHE 0.009 0.001 PHE B 181 TYR 0.015 0.001 TYR A 262 ARG 0.010 0.000 ARG D 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 1.900 Fit side-chains REVERT: A 52 ASP cc_start: 0.7808 (t0) cc_final: 0.6860 (t70) REVERT: A 54 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7578 (mtmm) REVERT: A 105 ASP cc_start: 0.8073 (t0) cc_final: 0.7854 (t0) REVERT: B 41 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8286 (mp) REVERT: B 79 ASP cc_start: 0.8576 (m-30) cc_final: 0.8368 (m-30) REVERT: C 79 ASP cc_start: 0.8674 (m-30) cc_final: 0.8448 (m-30) REVERT: E 79 ASP cc_start: 0.8514 (m-30) cc_final: 0.8305 (m-30) outliers start: 10 outliers final: 7 residues processed: 177 average time/residue: 1.1511 time to fit residues: 229.5649 Evaluate side-chains 168 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 177 optimal weight: 0.0470 overall best weight: 1.2482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN C 55 ASN C 183 ASN D 183 ASN E 55 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 17115 Z= 0.241 Angle : 0.620 13.640 23400 Z= 0.295 Chirality : 0.043 0.141 2760 Planarity : 0.005 0.036 2820 Dihedral : 8.979 118.321 2729 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.87 % Allowed : 17.75 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.19), residues: 1930 helix: 2.87 (0.17), residues: 775 sheet: -0.95 (0.23), residues: 440 loop : 0.41 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 456 HIS 0.003 0.001 HIS B 119 PHE 0.006 0.001 PHE E 265 TYR 0.021 0.001 TYR B 67 ARG 0.006 0.000 ARG B 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 1.869 Fit side-chains REVERT: A 52 ASP cc_start: 0.7474 (t0) cc_final: 0.6674 (t0) REVERT: A 105 ASP cc_start: 0.8149 (t0) cc_final: 0.7846 (t0) REVERT: A 184 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.5947 (pm20) REVERT: B 184 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.5852 (pm20) REVERT: B 242 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7802 (t80) REVERT: B 315 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7820 (mmm-85) REVERT: C 50 ASN cc_start: 0.7857 (t0) cc_final: 0.7539 (t0) REVERT: C 52 ASP cc_start: 0.6890 (t0) cc_final: 0.6460 (t0) REVERT: D 120 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7845 (mtp85) REVERT: D 184 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6139 (pm20) outliers start: 34 outliers final: 15 residues processed: 185 average time/residue: 1.1053 time to fit residues: 231.6936 Evaluate side-chains 171 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 453 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 183 ASN E 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 17115 Z= 0.272 Angle : 0.611 14.052 23400 Z= 0.289 Chirality : 0.044 0.143 2760 Planarity : 0.005 0.041 2820 Dihedral : 9.078 122.891 2717 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 4.07 % Allowed : 16.98 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 1930 helix: 2.45 (0.18), residues: 775 sheet: -1.07 (0.22), residues: 465 loop : 0.32 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 456 HIS 0.003 0.001 HIS B 119 PHE 0.007 0.001 PHE B 303 TYR 0.022 0.001 TYR B 67 ARG 0.006 0.000 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 161 time to evaluate : 1.990 Fit side-chains REVERT: A 52 ASP cc_start: 0.7307 (t0) cc_final: 0.6382 (t70) REVERT: A 105 ASP cc_start: 0.8147 (t0) cc_final: 0.7872 (t0) REVERT: A 184 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.5964 (pm20) REVERT: A 201 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7678 (mm) REVERT: A 311 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6033 (pp30) REVERT: B 52 ASP cc_start: 0.6788 (t70) cc_final: 0.6495 (t0) REVERT: B 99 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8154 (pp) REVERT: B 120 ARG cc_start: 0.8238 (mpp80) cc_final: 0.7546 (mmm-85) REVERT: B 184 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.5879 (pm20) REVERT: B 242 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7830 (t80) REVERT: B 315 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7848 (mmm-85) REVERT: C 201 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7678 (mm) REVERT: D 17 ASP cc_start: 0.7100 (m-30) cc_final: 0.6873 (m-30) REVERT: D 52 ASP cc_start: 0.6433 (t0) cc_final: 0.6111 (t0) REVERT: D 120 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7872 (mtp85) REVERT: D 184 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6165 (pm20) REVERT: E 52 ASP cc_start: 0.7182 (t70) cc_final: 0.6592 (t70) REVERT: E 122 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6875 (tt0) REVERT: E 311 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6893 (pp30) REVERT: E 328 ARG cc_start: 0.4743 (OUTLIER) cc_final: 0.4270 (mmm-85) outliers start: 74 outliers final: 28 residues processed: 216 average time/residue: 1.0682 time to fit residues: 262.2036 Evaluate side-chains 191 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 151 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 55 ASN Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 328 ARG Chi-restraints excluded: chain E residue 453 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 ASN D 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 17115 Z= 0.248 Angle : 0.603 13.567 23400 Z= 0.285 Chirality : 0.043 0.157 2760 Planarity : 0.005 0.039 2820 Dihedral : 8.987 122.514 2717 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.96 % Allowed : 17.31 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 1930 helix: 2.30 (0.18), residues: 775 sheet: -1.16 (0.22), residues: 465 loop : 0.28 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 456 HIS 0.003 0.001 HIS B 411 PHE 0.006 0.001 PHE D 199 TYR 0.021 0.001 TYR B 67 ARG 0.008 0.000 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 155 time to evaluate : 1.750 Fit side-chains REVERT: A 52 ASP cc_start: 0.7337 (t0) cc_final: 0.7065 (t0) REVERT: A 105 ASP cc_start: 0.8163 (t0) cc_final: 0.7886 (t0) REVERT: A 184 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.5968 (pm20) REVERT: A 201 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7678 (mm) REVERT: A 311 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6052 (pp30) REVERT: B 52 ASP cc_start: 0.6703 (t70) cc_final: 0.6196 (t0) REVERT: B 55 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7843 (m110) REVERT: B 116 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: B 120 ARG cc_start: 0.8285 (mpp80) cc_final: 0.7545 (mmm-85) REVERT: B 184 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.5886 (pm20) REVERT: B 242 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7817 (t80) REVERT: B 315 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7817 (mmm-85) REVERT: B 331 TRP cc_start: 0.7614 (t60) cc_final: 0.7317 (t60) REVERT: C 108 LYS cc_start: 0.8306 (mtmm) cc_final: 0.8038 (mtmm) REVERT: C 201 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7656 (mm) REVERT: D 52 ASP cc_start: 0.6373 (t0) cc_final: 0.6093 (t0) REVERT: D 99 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8057 (pp) REVERT: D 105 ASP cc_start: 0.8395 (t0) cc_final: 0.8143 (t0) REVERT: D 120 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7867 (mtp85) REVERT: D 184 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6109 (pm20) REVERT: E 52 ASP cc_start: 0.6968 (t70) cc_final: 0.6283 (t70) REVERT: E 122 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6871 (tt0) REVERT: E 311 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6882 (pp30) REVERT: E 328 ARG cc_start: 0.4737 (OUTLIER) cc_final: 0.4260 (mmm-85) outliers start: 72 outliers final: 31 residues processed: 211 average time/residue: 1.0789 time to fit residues: 260.0223 Evaluate side-chains 197 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 328 ARG Chi-restraints excluded: chain E residue 453 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 140 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN D 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17115 Z= 0.195 Angle : 0.583 13.493 23400 Z= 0.274 Chirality : 0.043 0.165 2760 Planarity : 0.005 0.044 2820 Dihedral : 8.771 121.157 2717 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.68 % Allowed : 18.08 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.19), residues: 1930 helix: 2.31 (0.18), residues: 775 sheet: -1.19 (0.22), residues: 465 loop : 0.28 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 456 HIS 0.002 0.001 HIS C 411 PHE 0.005 0.001 PHE C 233 TYR 0.020 0.001 TYR B 67 ARG 0.009 0.000 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 156 time to evaluate : 2.100 Fit side-chains REVERT: A 105 ASP cc_start: 0.8178 (t0) cc_final: 0.7684 (t0) REVERT: A 116 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: A 184 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.5965 (pm20) REVERT: A 201 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7716 (mm) REVERT: A 311 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6137 (pp30) REVERT: B 52 ASP cc_start: 0.6676 (t70) cc_final: 0.6286 (t0) REVERT: B 116 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8519 (m-80) REVERT: B 184 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.5895 (pm20) REVERT: B 242 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7779 (t80) REVERT: B 315 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7785 (mmm-85) REVERT: B 331 TRP cc_start: 0.7575 (t60) cc_final: 0.7222 (t60) REVERT: C 108 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7939 (mtmm) REVERT: C 201 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7841 (mm) REVERT: D 52 ASP cc_start: 0.6345 (t70) cc_final: 0.5859 (t0) REVERT: D 99 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8063 (pp) REVERT: D 105 ASP cc_start: 0.8310 (t0) cc_final: 0.8019 (t0) REVERT: D 120 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7854 (mtp85) REVERT: D 184 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6143 (pm20) REVERT: D 328 ARG cc_start: 0.4423 (OUTLIER) cc_final: 0.4174 (mmm-85) REVERT: E 52 ASP cc_start: 0.6895 (t70) cc_final: 0.6289 (t70) REVERT: E 108 LYS cc_start: 0.8265 (mtmm) cc_final: 0.7865 (mtmm) REVERT: E 311 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6879 (pp30) REVERT: E 328 ARG cc_start: 0.4704 (OUTLIER) cc_final: 0.4346 (mmm-85) outliers start: 67 outliers final: 28 residues processed: 208 average time/residue: 1.0539 time to fit residues: 249.6171 Evaluate side-chains 197 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 155 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 99 optimal weight: 0.0770 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 HIS D 183 ASN E 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17115 Z= 0.183 Angle : 0.579 13.474 23400 Z= 0.272 Chirality : 0.043 0.163 2760 Planarity : 0.004 0.039 2820 Dihedral : 8.596 120.461 2717 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.79 % Allowed : 18.41 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.19), residues: 1930 helix: 2.27 (0.18), residues: 775 sheet: -1.09 (0.22), residues: 455 loop : 0.27 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 456 HIS 0.002 0.001 HIS B 119 PHE 0.006 0.001 PHE C 242 TYR 0.019 0.001 TYR B 67 ARG 0.008 0.000 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 155 time to evaluate : 1.980 Fit side-chains REVERT: A 105 ASP cc_start: 0.8151 (t0) cc_final: 0.7653 (t0) REVERT: A 116 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8364 (m-80) REVERT: A 184 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.5964 (pm20) REVERT: A 311 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.6130 (pp30) REVERT: B 52 ASP cc_start: 0.6654 (t70) cc_final: 0.6291 (t0) REVERT: B 105 ASP cc_start: 0.8484 (t0) cc_final: 0.8108 (t0) REVERT: B 116 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8490 (m-80) REVERT: B 120 ARG cc_start: 0.8136 (mpp80) cc_final: 0.7566 (mmm-85) REVERT: B 184 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.5895 (pm20) REVERT: B 242 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7788 (t80) REVERT: B 315 ARG cc_start: 0.8167 (mtp85) cc_final: 0.7825 (mmm-85) REVERT: B 331 TRP cc_start: 0.7588 (t60) cc_final: 0.7210 (t60) REVERT: C 108 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7942 (mtmm) REVERT: C 201 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7815 (mm) REVERT: C 328 ARG cc_start: 0.4593 (OUTLIER) cc_final: 0.4167 (mmm-85) REVERT: D 52 ASP cc_start: 0.6341 (t70) cc_final: 0.5967 (t0) REVERT: D 99 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8031 (pp) REVERT: D 105 ASP cc_start: 0.8260 (t0) cc_final: 0.7961 (t0) REVERT: D 120 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7832 (mtp85) REVERT: D 184 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6124 (pm20) REVERT: E 52 ASP cc_start: 0.6908 (t70) cc_final: 0.6330 (t70) REVERT: E 108 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7827 (mtmm) REVERT: E 311 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6859 (pp30) REVERT: E 328 ARG cc_start: 0.4673 (OUTLIER) cc_final: 0.4383 (mmm-85) outliers start: 69 outliers final: 27 residues processed: 215 average time/residue: 1.0373 time to fit residues: 254.5372 Evaluate side-chains 197 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 157 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 158 optimal weight: 0.0020 chunk 105 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 ASN D 183 ASN E 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17115 Z= 0.150 Angle : 0.572 13.493 23400 Z= 0.269 Chirality : 0.042 0.176 2760 Planarity : 0.004 0.041 2820 Dihedral : 8.379 118.632 2717 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.69 % Allowed : 19.51 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.19), residues: 1930 helix: 2.29 (0.18), residues: 775 sheet: -1.07 (0.22), residues: 455 loop : 0.30 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 456 HIS 0.002 0.001 HIS B 119 PHE 0.005 0.001 PHE C 233 TYR 0.018 0.001 TYR B 67 ARG 0.010 0.000 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 166 time to evaluate : 2.026 Fit side-chains REVERT: A 79 ASP cc_start: 0.8418 (m-30) cc_final: 0.8160 (m-30) REVERT: A 105 ASP cc_start: 0.8125 (t0) cc_final: 0.7645 (t0) REVERT: A 116 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.8361 (m-80) REVERT: A 184 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.5915 (pm20) REVERT: A 319 ASP cc_start: 0.7913 (t0) cc_final: 0.7693 (t0) REVERT: A 328 ARG cc_start: 0.4602 (OUTLIER) cc_final: 0.4369 (mmm-85) REVERT: B 52 ASP cc_start: 0.6561 (t70) cc_final: 0.6195 (t0) REVERT: B 105 ASP cc_start: 0.8477 (t0) cc_final: 0.8107 (t0) REVERT: B 116 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8489 (m-80) REVERT: B 120 ARG cc_start: 0.8152 (mpp80) cc_final: 0.7591 (mmm-85) REVERT: B 184 GLN cc_start: 0.6809 (OUTLIER) cc_final: 0.5917 (pm20) REVERT: B 242 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7757 (t80) REVERT: B 315 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7802 (mmm-85) REVERT: B 331 TRP cc_start: 0.7591 (t60) cc_final: 0.7200 (t60) REVERT: C 108 LYS cc_start: 0.8186 (mtmm) cc_final: 0.7915 (mtmm) REVERT: C 201 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7781 (mm) REVERT: C 328 ARG cc_start: 0.4655 (OUTLIER) cc_final: 0.4117 (mtt-85) REVERT: D 52 ASP cc_start: 0.6376 (t70) cc_final: 0.5982 (t0) REVERT: D 99 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7994 (pp) REVERT: D 105 ASP cc_start: 0.8199 (t0) cc_final: 0.7900 (t0) REVERT: D 120 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7833 (mtp85) REVERT: D 184 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6189 (pm20) REVERT: E 52 ASP cc_start: 0.6962 (t70) cc_final: 0.6411 (t70) REVERT: E 92 SER cc_start: 0.9061 (m) cc_final: 0.8616 (p) REVERT: E 108 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7716 (mtmm) REVERT: E 122 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6853 (tt0) REVERT: E 311 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6890 (pp30) REVERT: E 328 ARG cc_start: 0.4754 (OUTLIER) cc_final: 0.4292 (mmm-85) outliers start: 49 outliers final: 21 residues processed: 205 average time/residue: 1.0363 time to fit residues: 242.4253 Evaluate side-chains 194 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 159 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 17 optimal weight: 0.0970 chunk 147 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 ASN D 183 ASN E 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17115 Z= 0.191 Angle : 0.586 13.439 23400 Z= 0.275 Chirality : 0.043 0.168 2760 Planarity : 0.004 0.042 2820 Dihedral : 8.338 119.217 2717 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.86 % Allowed : 19.45 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.19), residues: 1930 helix: 2.24 (0.18), residues: 775 sheet: -1.06 (0.22), residues: 455 loop : 0.28 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 456 HIS 0.002 0.001 HIS B 119 PHE 0.006 0.001 PHE C 233 TYR 0.020 0.001 TYR B 67 ARG 0.009 0.000 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 164 time to evaluate : 1.849 Fit side-chains REVERT: A 52 ASP cc_start: 0.7107 (t0) cc_final: 0.6396 (t0) REVERT: A 79 ASP cc_start: 0.8408 (m-30) cc_final: 0.8180 (m-30) REVERT: A 105 ASP cc_start: 0.8143 (t0) cc_final: 0.7656 (t0) REVERT: A 116 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: A 184 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.5923 (pm20) REVERT: A 319 ASP cc_start: 0.7950 (t0) cc_final: 0.7708 (t0) REVERT: B 52 ASP cc_start: 0.6548 (t70) cc_final: 0.6205 (t0) REVERT: B 105 ASP cc_start: 0.8492 (t0) cc_final: 0.8112 (t0) REVERT: B 116 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8488 (m-80) REVERT: B 120 ARG cc_start: 0.8165 (mpp80) cc_final: 0.7594 (mmm-85) REVERT: B 184 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.5893 (pm20) REVERT: B 242 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7764 (t80) REVERT: B 315 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7778 (mmm-85) REVERT: B 331 TRP cc_start: 0.7612 (t60) cc_final: 0.7187 (t60) REVERT: B 418 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6304 (mt-10) REVERT: C 108 LYS cc_start: 0.8191 (mtmm) cc_final: 0.7914 (mtmm) REVERT: C 201 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7794 (mm) REVERT: D 52 ASP cc_start: 0.6366 (t70) cc_final: 0.6041 (t0) REVERT: D 99 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.8016 (pp) REVERT: D 105 ASP cc_start: 0.8173 (t0) cc_final: 0.7869 (t0) REVERT: D 120 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7852 (mtp85) REVERT: D 184 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6252 (pm20) REVERT: E 52 ASP cc_start: 0.7046 (t70) cc_final: 0.6291 (t70) REVERT: E 92 SER cc_start: 0.9065 (m) cc_final: 0.8618 (p) REVERT: E 108 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7704 (mtmm) REVERT: E 122 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: E 311 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6886 (pp30) REVERT: E 328 ARG cc_start: 0.4772 (OUTLIER) cc_final: 0.4492 (mmm-85) outliers start: 52 outliers final: 26 residues processed: 206 average time/residue: 1.0812 time to fit residues: 252.8500 Evaluate side-chains 197 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 158 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 ASN D 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17115 Z= 0.245 Angle : 0.605 13.365 23400 Z= 0.284 Chirality : 0.043 0.170 2760 Planarity : 0.005 0.044 2820 Dihedral : 8.390 121.081 2717 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.58 % Allowed : 19.89 % Favored : 77.53 % 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: 0.98 (0.19), residues: 1930 helix: 2.20 (0.18), residues: 780 sheet: -1.09 (0.22), residues: 455 loop : 0.25 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 456 HIS 0.003 0.001 HIS B 119 PHE 0.006 0.001 PHE C 233 TYR 0.021 0.001 TYR B 67 ARG 0.009 0.000 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 154 time to evaluate : 2.032 Fit side-chains REVERT: A 52 ASP cc_start: 0.7147 (t0) cc_final: 0.6364 (t0) REVERT: A 105 ASP cc_start: 0.8161 (t0) cc_final: 0.7659 (t0) REVERT: A 116 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: A 184 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.5996 (pm20) REVERT: A 319 ASP cc_start: 0.8056 (t0) cc_final: 0.7805 (t0) REVERT: B 52 ASP cc_start: 0.6584 (t70) cc_final: 0.6232 (t0) REVERT: B 105 ASP cc_start: 0.8477 (t0) cc_final: 0.8100 (t0) REVERT: B 116 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8542 (m-80) REVERT: B 120 ARG cc_start: 0.8183 (mpp80) cc_final: 0.7613 (mmm-85) REVERT: B 184 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.5919 (pm20) REVERT: B 242 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7780 (t80) REVERT: B 315 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7786 (mmm-85) REVERT: B 331 TRP cc_start: 0.7620 (t60) cc_final: 0.7158 (t60) REVERT: B 418 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6335 (mt-10) REVERT: C 108 LYS cc_start: 0.8196 (mtmm) cc_final: 0.7922 (mtmm) REVERT: C 201 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7793 (mm) REVERT: D 52 ASP cc_start: 0.6438 (t70) cc_final: 0.5978 (t0) REVERT: D 99 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8056 (pp) REVERT: D 105 ASP cc_start: 0.8161 (t0) cc_final: 0.7843 (t0) REVERT: D 120 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7846 (mtp85) REVERT: D 184 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6079 (pm20) REVERT: E 52 ASP cc_start: 0.6950 (t70) cc_final: 0.6345 (t70) REVERT: E 92 SER cc_start: 0.9062 (m) cc_final: 0.8603 (p) REVERT: E 108 LYS cc_start: 0.8158 (mtmm) cc_final: 0.7702 (mtmm) REVERT: E 122 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6883 (tt0) REVERT: E 311 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6873 (pp30) REVERT: E 328 ARG cc_start: 0.4879 (OUTLIER) cc_final: 0.4472 (mmm-85) outliers start: 47 outliers final: 31 residues processed: 193 average time/residue: 1.0652 time to fit residues: 233.7697 Evaluate side-chains 198 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 154 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 194 optimal weight: 4.9990 chunk 178 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17115 Z= 0.200 Angle : 0.596 13.369 23400 Z= 0.280 Chirality : 0.043 0.169 2760 Planarity : 0.004 0.043 2820 Dihedral : 8.340 120.902 2717 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.31 % Allowed : 20.27 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.19), residues: 1930 helix: 2.21 (0.18), residues: 780 sheet: -1.09 (0.22), residues: 455 loop : 0.28 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 456 HIS 0.002 0.001 HIS B 411 PHE 0.006 0.001 PHE C 233 TYR 0.020 0.001 TYR B 67 ARG 0.009 0.000 ARG C 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 155 time to evaluate : 1.764 Fit side-chains REVERT: A 52 ASP cc_start: 0.7138 (t0) cc_final: 0.6308 (t0) REVERT: A 54 LYS cc_start: 0.7765 (mtmm) cc_final: 0.7356 (mtmt) REVERT: A 105 ASP cc_start: 0.8159 (t0) cc_final: 0.7662 (t0) REVERT: A 116 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: A 184 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.5983 (pm20) REVERT: B 52 ASP cc_start: 0.6576 (t70) cc_final: 0.6215 (t0) REVERT: B 105 ASP cc_start: 0.8497 (t0) cc_final: 0.8115 (t0) REVERT: B 116 TYR cc_start: 0.8780 (OUTLIER) cc_final: 0.8533 (m-80) REVERT: B 120 ARG cc_start: 0.8186 (mpp80) cc_final: 0.7628 (mmm-85) REVERT: B 184 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.5916 (pm20) REVERT: B 242 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7760 (t80) REVERT: B 315 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7777 (mmm-85) REVERT: B 331 TRP cc_start: 0.7625 (t60) cc_final: 0.7158 (t60) REVERT: B 418 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6327 (mt-10) REVERT: C 108 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7909 (mtmm) REVERT: C 201 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7794 (mm) REVERT: D 52 ASP cc_start: 0.6385 (t70) cc_final: 0.5992 (t0) REVERT: D 99 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8058 (pp) REVERT: D 105 ASP cc_start: 0.8166 (t0) cc_final: 0.7853 (t0) REVERT: D 120 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7852 (mtp85) REVERT: D 184 GLN cc_start: 0.6973 (OUTLIER) cc_final: 0.6123 (pm20) REVERT: E 52 ASP cc_start: 0.6936 (t70) cc_final: 0.6339 (t70) REVERT: E 92 SER cc_start: 0.9053 (m) cc_final: 0.8608 (p) REVERT: E 108 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7784 (mtmm) REVERT: E 122 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6964 (tt0) REVERT: E 311 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6936 (pp30) REVERT: E 328 ARG cc_start: 0.4893 (OUTLIER) cc_final: 0.4495 (mmm-85) outliers start: 42 outliers final: 28 residues processed: 191 average time/residue: 1.1034 time to fit residues: 238.7669 Evaluate side-chains 193 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 152 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 328 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.098039 restraints weight = 21147.927| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.41 r_work: 0.3024 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17115 Z= 0.192 Angle : 0.591 13.397 23400 Z= 0.277 Chirality : 0.043 0.175 2760 Planarity : 0.004 0.043 2820 Dihedral : 8.259 120.940 2717 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.42 % Allowed : 20.16 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.19), residues: 1930 helix: 2.23 (0.18), residues: 780 sheet: -1.07 (0.22), residues: 455 loop : 0.28 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 456 HIS 0.002 0.001 HIS B 119 PHE 0.006 0.001 PHE C 233 TYR 0.020 0.001 TYR B 67 ARG 0.009 0.000 ARG C 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4762.97 seconds wall clock time: 85 minutes 33.72 seconds (5133.72 seconds total)